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1. Detection of Anaplasma and Ehrlichia bacteria in humans, wildlife, and ticks in the Amazon rainforest

Author: Marie Buysse, Rachid Koual, Florian Binetruy, Benoit de Thoisy, Xavier Baudrimont, Stéphane Garnier, Maylis Douine, Christine Chevillon, Frédéric Delsuc, François Catzeflis, Didier Bouchon, and Olivier Duron
Subjects: Science
Abstract: Abstract Tick-borne bacteria of the genera Ehrlichia and Anaplasma cause several emerging human infectious diseases worldwide. In this study, we conduct an extensive survey for Ehrlichia and Anaplasma infections in the rainforests of the Amazon biome of French Guiana. Through molecular genetics and metagenomics reconstruction, we observe a high indigenous biodiversity of infections circulating among humans, wildlife, and ticks inhabiting these ecosystems. Molecular typing identifies these infections as highly endemic, with a majority of new strains and putative species specific to French Guiana. They are detected in unusual rainforest wild animals, suggesting they have distinctive sylvatic transmission cycles. They also present potential health hazards, as revealed by the detection of Candidatus Anaplasma sparouinense in human red blood cells and that of a new close relative of the human pathogen Ehrlichia ewingii, Candidatus Ehrlichia cajennense, in the tick species that most frequently bite humans in South America. The genome assembly of three new putative species obtained from human, sloth, and tick metagenomes further reveals the presence of major homologs of Ehrlichia and Anaplasma virulence factors. These observations converge to classify health hazards associated with Ehrlichia and Anaplasma infections in the Amazon biome as distinct from those in the Northern Hemisphere.
Published: 2024
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2. The role of health mediation in investigation of Hantavirus cases among informal settlements inhabitants of Cayenne area, French Guiana, 2022–2023

Author: Margot Oberlis, Marion Guyot, Paul Le Turnier, Luisiane Carvalho, Tiphanie Succo, Dominique Rousset, Benoit De Thoisy, Mélanie Gaillet, Anne Lavergne, Stéphanie Vandentorren, and Loïc Epelboin
Subjects: investigation, Hantavirus, health mediation, socially vulnerable people, informal settlement, Public aspects of medicine, RA1-1270
Abstract: ContextIn 2022, four severe cases of Hantavirus pulmonary syndrome (HPS) were reported in patients from informal settlements around Cayenne, the main city in French Guiana. Regional Health Agency (RHA) was commissioned by the French Public Health Agency to estimate the seroprevalence of Hantavirus infections in the neighborhoods of confirmed cases of HPS. RHA then commissioned the French Red Cross (FRC) mobile public health team, providing support in environmental health issues to the population living in informal settlements by health mediators, to facilitate the investigation. The objective of this study was to describe the health mediators' activities set up to improve the efficiency of the investigation.MethodsThe health mediators' team was specifically trained by virologist and infectiologist specialized in HPS. They helped the investigating team and health workers at various steps of the investigation. These interventions are then described in the results section.ResultsThe investigation took place between Nov. 2022 and March 2023 in three neighborhoods. During the pre-investigation activities, the mediators raised awareness about HPS of 343 people, among whom 319 (93%) planned to participate in the investigation. Altogether, 274 people finally participated in the investigation, including, i.e., 30.8% of the estimated population living in the three concerned settlements. The global proportion of patients with positive IgG anti-Hantavirus was 5.1%. The health mediators team supported the following steps: preliminary meetings and training modules, identification of resource persons, field visits and awareness and information campaigns (pre-investigation); on field data collection in informal settlements (per-investigation) and communication of individual results, public feedback meeting (post-investigation).Discussion/ConclusionThe involvement of mediators was probably a factor in the success of the public health response to socially vulnerable people living in the investigated neighborhoods. The preliminary prevention activities helped to raise awareness of the health risk and to enroll participants. Health mediation and outreach activities seem relevant tools of epidemiological field investigations in diseases affecting inhabitants of informal settlements.
Published: 2024
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3. Mosquito Feeding Habits in Coastal French Guiana: Mammals in the Crosshairs?

Author: Amandine Guidez, Sourakhata Tirera, Stanislas Talaga, Guillaume Lacour, Romuald Carinci, Edith Darcissac, Damien Donato, Pascal Gaborit, Emmanuelle Clervil, Yanouk Epelboin, Benoit de Thoisy, Isabelle Dusfour, Jean-Bernard Duchemin, and Anne Lavergne
Subjects: mosquito feeding habits, blood-fed females, host associations, French Guiana, Science
Abstract: Pathogens transmitted by mosquitoes (Diptera, Culicidae) in sylvatic or urban cycles involve wild or domestic animals and humans, driven by various mosquito species with distinct host preferences. Understanding mosquito–host associations is crucial for ecological insights and pathogen surveillance. In this study, we analyzed mosquito blood meals from coastal French Guiana by amplifying and sequencing host DNA from blood-fed females. Using the 12S ribosomal RNA gene and Sanger sequencing, we identified blood meals from 26 mosquito species across six genera, with 59% belonging to the Culex genus. Nanopore sequencing of selected samples showed 12 mosquito species with one to three mixed blood-meal sources. Mammals were the primary hosts (88%), followed by birds (7%), squamates (3%), and amphibians (2%), indicating a strong preference for mammalian hosts. A total of 46 vertebrate host species were identified, demonstrating high host diversity. This research provides insights into mosquito host usage and highlights the complexities of monitoring arboviruses of public health concern.
Published: 2024
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4. Glironia venusta (Thomas, 1912) (Didelphidae) reaches the Atlantic! New records in French Guiana, with notes on behaviour

Author: Paul Alexandre and Benoit de Thoisy
Subjects: Amazonia, biogeography, distribution, marsupial, Biology (General), QH301-705.5
Abstract: We report observations of Glironia venusta Thomas, 1912, Bushy-tailed Opossum, from coastal French Guiana, expanding the distribution of this species 300 km north of its previously known range.
Published: 2023
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5. Revalidation of Passalites Gloger, 1841 for the Amazon brown brocket deer P. nemorivagus (Cuvier, 1817) (Mammalia, Artiodactyla, Cervidae)

Author: Jorge Alfonso Morales-Donoso, Gabrielle Queiroz Vacari, Agda Maria Bernegossi, Eluzai Dinai Pinto Sandoval, Pedro Henrique Faria Peres, David Javier Galindo, Benoit de Thoisy, Miluse Vozdova, Svatava Kubickova, and José Mauricio Barbanti Duarte
Subjects: Zoology, QL1-991
Abstract: Mazama nemorivaga (Cuvier, 1817) is a gray brocket deer that inhabits the Amazon region. An assessment of previous studies revealed inconsistencies in its current taxonomic classification, suggesting the need for an update in its genus classification. A taxonomic repositioning of this species is proposed through the collection of a specimen from its type locality (French Guiana) with subsequent morphological (coloring pattern, body measurements, and craniometry), cytogenetics (G Band, C Band, conventional Giemsa, Ag-NOR staining, and BAC probe mapping), and molecular phylogenetic analysis (mitochondrial genes Cyt B of 920 bp, COI I of 658 bp, D-loop 610 bp), and comparisons with other specimens of the same taxon, as well as other Neotropical deer species. The morphological and cytogenetic differences between this and other Neotropical Cervidae confirm the taxon as a unique and valid species. The phylogenetic analysis evidenced the basal position of the M. nemorivaga specimens within the Blastocerina clade. This shows early diversification and wide divergence from the other species, suggesting that the taxon should be transferred to a different genus. A taxonomic update of the genus name is proposed through the validation of Passalites Gloger, 1841, with Passalites nemorivagus (Cuvier, 1817) as the type species. Future research should focus on evaluating the potential existence of other species within the genus Passalites, as suggested in the literature.
Published: 2023
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6. Metagenomics uncovers dietary adaptations for chitin digestion in the gut microbiota of convergent myrmecophagous mammals

Author: Sophie Teullet, Marie-Ka Tilak, Amandine Magdeleine, Roxane Schaub, Nora M. Weyer, Wendy Panaino, Andrea Fuller, W. J. Loughry, Nico L. Avenant, Benoit de Thoisy, Guillaume Borrel, and Frédéric Delsuc
Subjects: convergent evolution, myrmecophagy, mammals, gut microbiota, chitinases, metagenomics, Microbiology, QR1-502
Abstract: ABSTRACT In mammals, myrmecophagy (ant and termite consumption) represents a striking example of dietary convergence. This trait evolved independently at least five times in placentals with myrmecophagous species comprising aardvarks, anteaters, some armadillos, pangolins, and aardwolves. The gut microbiome plays an important role in dietary adaptation, and previous analyses of 16S rRNA metabarcoding data have revealed convergence in the composition of the gut microbiota among some myrmecophagous species. However, the functions performed by these gut bacterial symbionts and their potential role in the digestion of prey chitinous exoskeletons remain open questions. Using long- and short-read sequencing of fecal samples, we generated 29 gut metagenomes from nine myrmecophagous and closely related insectivorous species sampled in French Guiana, South Africa, and the United States. From these, we reconstructed 314 high-quality bacterial genome bins of which 132 carried chitinase genes, highlighting their potential role in insect prey digestion. These chitinolytic bacteria belonged mainly to the family Lachnospiraceae, and some were likely convergently recruited in the different myrmecophagous species as they were detected in several host orders (i.e., Enterococcus faecalis, Blautia sp.), suggesting that they could be directly involved in the adaptation to myrmecophagy. Others were found to be more host-specific, possibly reflecting phylogenetic constraints and environmental influences. Overall, our results highlight the potential role of the gut microbiome in chitin digestion in myrmecophagous mammals and provide the basis for future comparative studies performed at the mammalian scale to further unravel the mechanisms underlying the convergent adaptation to myrmecophagy. Importance Myrmecophagous mammals are specialized in the consumption of ants and/or termites. They do not share a direct common ancestor and evolved convergently in five distinct placental orders raising questions about the underlying adaptive mechanisms involved and the relative contribution of natural selection and phylogenetic constraints. Understanding how these species digest their prey can help answer these questions. More specifically, the role of their gut microbial symbionts in the digestion of the insect chitinous exoskeleton has not been investigated in all myrmecophagous orders. We generated 29 new gut metagenomes from nine myrmecophagous species to reconstruct more than 300 bacterial genomes in which we identified chitin-degrading enzymes. Studying the distribution of these chitinolytic bacteria among hosts revealed both shared and specific bacteria between ant-eating species. Overall, our results highlight the potential role of gut symbionts in the convergent dietary adaptation of myrmecophagous mammals and the evolutionary mechanisms shaping their gut microbiota.
Published: 2023
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7. Review on Main Arboviruses Circulating on French Guiana, An Ultra-Peripheric European Region in South America

Author: Timothee Bonifay, Paul Le Turnier, Yanouk Epelboin, Luisiane Carvalho, Benoit De Thoisy, Félix Djossou, Jean-Bernard Duchemin, Philippe Dussart, Antoine Enfissi, Anne Lavergne, Rémi Mutricy, Mathieu Nacher, Sébastien Rabier, Stanislas Talaga, Antoine Talarmin, Dominique Rousset, and Loïc Epelboin
Subjects: arbovirus, French Guiana, Dengue virus, Chikungunya virus, Zika virus, Yellow fever virus, Microbiology, QR1-502
Abstract: French Guiana (FG), a French overseas territory in South America, is susceptible to tropical diseases, including arboviruses. The tropical climate supports the proliferation and establishment of vectors, making it difficult to control transmission. In the last ten years, FG has experienced large outbreaks of imported arboviruses such as Chikungunya and Zika, as well as endemic arboviruses such as dengue, Yellow fever, and Oropouche virus. Epidemiological surveillance is challenging due to the differing distributions and behaviors of vectors. This article aims to summarize the current knowledge of these arboviruses in FG and discuss the challenges of arbovirus emergence and reemergence. Effective control measures are hampered by the nonspecific clinical presentation of these diseases, as well as the Aedes aegypti mosquito’s resistance to insecticides. Despite the high seroprevalence of certain viruses, the possibility of new epidemics cannot be ruled out. Therefore, active epidemiological surveillance is needed to identify potential outbreaks, and an adequate sentinel surveillance system and broad virological diagnostic panel are being developed in FG to improve disease management.
Published: 2023
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8. Designation of a neotype for Mazama americana (Artiodactyla, Cervidae) reveals a cryptic new complex of brocket deer species

Author: Analorena Cifuentes-Rincón, Jorge Alfonso Morales-Donoso, Eluzai Dinai Pinto Sandoval, Iara Maluf Tomazella, Aline Meira Bonfim Mantellatto, Benoit de Thoisy, and José Maurício Barbanti Duarte
Subjects: Zoology, QL1-991
Abstract: Mazama americana (red brocket deer) is the genus-type species (first species described for this genus) and the basis for the identity of other Mazama species. Mazama americana is one of the most abundant and widely distributed deer species in the neotropical forest. However, recent studies suggest that this taxon belongs to a species complex. Our goal was to collect an animal at the type locality (topotype) in French Guiana with the aim of characterizing the morphological (biometric, craniometric), cytogenetic (Giemsa, C-banding, G-banding and NOR) and molecular (mitochondrial DNA) features. The comparisons showed that the collected specimen was very similar morphologically to specimens from other South American populations, but it was cytogenetically and molecularly very different from any of the cytotypes already described for this species, corroborating the existence of a complex of cryptic species. The data suggest that the M. americana topotype is a different species from all the cytotypes already described in the literature and which occupy the southern region of the Amazon River. The characterization and designation of the M. americana neotype is the first step toward a taxonomic reorganization of the genus Mazama, with the potential identification of new species.
Published: 2020
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9. Recent sylvatic yellow fever virus transmission in Brazil: the news from an old disease

Author: Natalia Ingrid Oliveira Silva, Lívia Sacchetto, Izabela Maurício de Rezende, Giliane de Souza Trindade, Angelle Desiree LaBeaud, Benoit de Thoisy, and Betânia Paiva Drumond
Subjects: Yellow fever virus, Yellow fever, Arbovirus, Flavivirus, Non-human primate, Epizootic, Infectious and parasitic diseases, RC109-216
Abstract: Abstract Yellow fever (YF) is an acute viral disease, affecting humans and non-human primates (NHP), caused by the yellow fever virus (YFV). Despite the existence of a safe vaccine, YF continues to cause morbidity and mortality in thousands of people in Africa and South America. Since 2016, massive YF outbreaks have taken place in Brazil, reaching YF–free zones, causing thousands of deaths of humans and NHP. Here we reviewed the main epidemiological aspects, new clinical findings in humans, and issues regarding YFV infection in vectors and NHP in Brazil. The 2016–2019 YF epidemics have been considered the most significant outbreaks of the last 70 years in the country, and the number of human cases was 2.8 times higher than total cases in the previous 36 years. A new YFV lineage was associated with the recent outbreaks, with persistent circulation in Southeast Brazil until 2019. Due to the high number of infected patients, it was possible to evaluate severity and death predictors and new clinical features of YF. Haemagogus janthinomys and Haemagogus leucocelaenus were considered the primary vectors during the outbreaks, and no human case suggested the occurrence of the urban transmission cycle. YFV was detected in a variety of NHP specimens presenting viscerotropic disease, similar to that described experimentally. Further studies regarding NHP sensitivity to YFV, YF pathogenesis, and the duration of the immune response in NHP could contribute to YF surveillance, control, and future strategies for NHP conservation.
Published: 2020
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10. Large-scale population disappearances and cycling in the white-lipped peccary, a tropical forest mammal

Author: José M. V. Fragoso, André P. Antunes, Kirsten M. Silvius, Pedro A. L. Constantino, Galo Zapata-Ríos, Hani R. El Bizri, Richard E. Bodmer, Micaela Camino, Benoit de Thoisy, Robert B. Wallace, Thais Q. Morcatty, Pedro Mayor, Cecile Richard-Hansen, Mathew T. Hallett, Rafael A. Reyna-Hurtado, H. Harald Beck, Soledad de Bustos, Alexine Keuroghlian, Alessandra Nava, Olga L. Montenegro, Ennio Painkow Neto, and Mariana Altrichter
Subjects: Medicine, Science
Abstract: Many vertebrate species undergo population fluctuations that may be random or regularly cyclic in nature. Vertebrate population cycles in northern latitudes are driven by both endogenous and exogenous factors. Suggested causes of mysterious disappearances documented for populations of the Neotropical, herd-forming, white-lipped peccary (Tayassu pecari, henceforth “WLP”) include large-scale movements, overhunting, extreme floods, or disease outbreaks. By analyzing 43 disappearance events across the Neotropics and 88 years of commercial and subsistence harvest data for the Amazon, we show that WLP disappearances are widespread and occur regularly and at large spatiotemporal scales throughout the species’ range. We present evidence that the disappearances represent 7–12-year troughs in 20–30-year WLP population cycles occurring synchronously at regional and perhaps continent-wide spatial scales as large as 10,000–5 million km2. This may represent the first documented case of natural population cyclicity in a Neotropical mammal. Because WLP populations often increase dramatically prior to a disappearance, we posit that their population cycles result from over-compensatory, density-dependent mortality. Our data also suggest that the increase phase of a WLP cycle is partly dependent on recolonization from proximal, unfragmented and undisturbed forests. This highlights the importance of very large, continuous natural areas that enable source-sink population dynamics and ensure re-colonization and local population persistence in time and space.
Published: 2022

11. Neighbor danger: Yellow fever virus epizootics in urban and urban-rural transition areas of Minas Gerais state, during 2017-2018 yellow fever outbreaks in Brazil.

Author: Lívia Sacchetto, Natalia Ingrid Oliveira Silva, Izabela Maurício de Rezende, Matheus Soares Arruda, Thais Alkifeles Costa, Érica Munhoz de Mello, Gabriela Fernanda Garcia Oliveira, Pedro Augusto Alves, Vítor Emídio de Mendonça, Rodolfo German Antonelli Vidal Stumpp, Alaine Izabela Alves Prado, Adriano Pereira Paglia, Fernando Araújo Perini, Maurício Lacerda Nogueira, Erna Geessien Kroon, Benoit de Thoisy, Giliane de Souza Trindade, and Betânia Paiva Drumond
Subjects: Arctic medicine. Tropical medicine, RC955-962, Public aspects of medicine, RA1-1270
Abstract: BackgroundFrom the end of 2016 until the beginning of 2019, Brazil faced a massive sylvatic yellow fever (YF) outbreak. The 2016-2019 YF epidemics affected densely populated areas, especially the Southeast region, causing thousands of deaths of humans and non-human primates (NHP).Methodology/principal findingsWe conducted a molecular investigation of yellow fever virus (YFV) RNA in 781 NHP carcasses collected in the urban, urban-rural interface, and rural areas of Minas Gerais state, from January 2017 to December 2018. Samples were analyzed according to the period of sampling, NHP genera, sampling areas, and sampling areas/NHP genera to compare the proportions of YFV-positive carcasses and the estimated YFV genomic loads. YFV infection was confirmed in 38.1% of NHP carcasses (including specimens of the genera Alouatta, Callicebus, Callithrix, and Sapajus), from the urban, urban-rural interface, and rural areas. YFV RNA detection was positively associated with epidemic periods (especially from December to March) and the rural environment. Higher median viral genomic loads (one million times) were estimated in carcasses collected in rural areas compared to urban ones.Conclusions/significanceThe results showed the wide occurrence of YF in Minas Gerais in epidemic and non-epidemic periods. According to the sylvatic pattern of YF, a gradient of viral dissemination from rural towards urban areas was observed. A high YF positivity was observed for NHP carcasses collected in urban areas with a widespread occurrence in 67 municipalities of Minas Gerais, including large urban centers. Although there was no documented case of urban/Aedes YFV transmission to humans in Brazil during the 2016-2019 outbreaks, YFV-infected NHP in urban areas with high infestation by Aedes aegypti poses risks for YFV urban/Aedes transmission and urbanization.
Published: 2020
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12. Spatial epidemiology of yellow fever: Identification of determinants of the 2016-2018 epidemics and at-risk areas in Brazil.

Author: Benoit de Thoisy, Natalia Ingrid Oliveira Silva, Lívia Sacchetto, Giliane de Souza Trindade, and Betânia Paiva Drumond
Subjects: Arctic medicine. Tropical medicine, RC955-962, Public aspects of medicine, RA1-1270
Abstract: Optimise control strategies of infectious diseases, identify factors that favour the circulation of pathogens, and propose risk maps are crucial challenges for global health. Ecological niche modelling, once relying on an adequate framework and environmental descriptors can be a helpful tool for such purposes. Despite the existence of a vaccine, yellow fever (YF) is still a public health issue. Brazil faced massive sylvatic YF outbreaks from the end of 2016 up to mid-2018, but cases in human and non-human primates have been recorded until the beginning of 2020. Here we used both human and monkey confirmed YF cases from two epidemic periods (2016/2017 and 2017/2018) to describe the spatial distribution of the cases and explore how biotic and abiotic factors drive their occurrence. The distribution of YF cases largely overlaps for humans and monkeys, and a contraction of the spatial extent associated with a southward displacement is observed during the second period of the epidemics. More contributive variables to the spatiotemporal heterogeneity of cases were related to biotic factors (mammal richness), abiotic factors (temperature and precipitation), and some human-related variables (population density, human footprint, and human vaccination coverage). Both projections of the most favourable conditions showed similar trends with a contraction of the more at-risk areas. Once extrapolated at a large scale, the Amazon basin remains at lower risk, although surrounding forest regions and notably the North-West region, would face a higher risk. Spatial projections of infectious diseases often relied on climatic variables only; here for both models, we instead highlighted the importance of considering local biotic conditions, hosts vulnerability, social and epidemiological factors to run the spatial risk analysis correctly: all YF cases occurring later on, in 2019 and 2020, were observed in the predicted at-risk areas.
Published: 2020
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13. Comparative masticatory myology in anteaters and its implications for interpreting morphological convergence in myrmecophagous placentals

Author: Sérgio Ferreira-Cardoso, Pierre-Henri Fabre, Benoit de Thoisy, Frédéric Delsuc, and Lionel Hautier
Subjects: Masticatory apparatus, Anteaters, Myrmecophagy, Myology, Comparative anatomy, Convergence, Medicine, Biology (General), QH301-705.5
Abstract: Background Ecological adaptations of mammals are reflected in the morphological diversity of their feeding apparatus, which includes differences in tooth crown morphologies, variation in snout size, or changes in muscles of the feeding apparatus. The adaptability of their feeding apparatus allowed them to optimize resource exploitation in a wide range of habitats. The combination of computer-assisted X-ray microtomography (µ-CT) with contrast-enhancing staining protocols has bolstered the reconstruction of three-dimensional (3D) models of muscles. This new approach allows for accurate descriptions of muscular anatomy, as well as the quick measurement of muscle volumes and fiber orientation. Ant- and termite-eating (myrmecophagy) represents a case of extreme feeding specialization, which is usually accompanied by tooth reduction or complete tooth loss, snout elongation, acquisition of a long vermiform tongue, and loss of the zygomatic arch. Many of these traits evolved independently in distantly-related mammalian lineages. Previous reports on South American anteaters (Vermilingua) have shown major changes in the masticatory, intermandibular, and lingual muscular apparatus. These changes have been related to a functional shift in the role of upper and lower jaws in the evolutionary context of their complete loss of teeth and masticatory ability. Methods We used an iodine staining solution (I2KI) to perform contrast-enhanced µ-CT scanning on heads of the pygmy (Cyclopes didactylus), collared (Tamandua tetradactyla) and giant (Myrmecophaga tridactyla) anteaters. We reconstructed the musculature of the feeding apparatus of the three extant anteater genera using 3D reconstructions complemented with classical dissections of the specimens. We performed a description of the musculature of the feeding apparatus in the two morphologically divergent vermilinguan families (Myrmecophagidae and Cyclopedidae) and compared it to the association of morphological features found in other myrmecophagous placentals. Results We found that pygmy anteaters (Cyclopes) present a relatively larger and architecturally complex temporal musculature than that of collared (Tamandua) and giant (Myrmecophaga) anteaters, but shows a reduced masseter musculature, including the loss of the deep masseter. The loss of this muscle concurs with the loss of the jugal bone in Cyclopedidae. We show that anteaters, pangolins, and aardvarks present distinct anatomies despite morphological and ecological convergences.
Published: 2020
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14. The Influence of Habitat on Viral Diversity in Neotropical Rodent Hosts

Author: Sourakhata Tirera, Benoit de Thoisy, Damien Donato, Christiane Bouchier, Vincent Lacoste, Alain Franc, and Anne Lavergne
Subjects: virome, alpha diversity, rodents, Amazonia, viral ecology, viral phylogenies, Microbiology, QR1-502
Abstract: Rodents are important reservoirs of numerous viruses, some of which have significant impacts on public health. Ecosystem disturbances and decreased host species richness have been associated with the emergence of zoonotic diseases. In this study, we aimed at (a) characterizing the viral diversity in seven neotropical rodent species living in four types of habitats and (b) exploring how the extent of environmental disturbance influences this diversity. Through a metagenomic approach, we identified 77,767 viral sequences from spleen, kidney, and serum samples. These viral sequences were attributed to 27 viral families known to infect vertebrates, invertebrates, plants, and amoeba. Viral diversities were greater in pristine habitats compared with disturbed ones, and lowest in peri-urban areas. High viral richness was observed in savannah areas. Differences in these diversities were explained by rare viruses that were generally more frequent in pristine forest and savannah habitats. Moreover, changes in the ecology and behavior of rodent hosts, in a given habitat, such as modifications to the diet in disturbed vs. pristine forests, are major determinants of viral composition. Lastly, the phylogenetic relationships of four vertebrate-related viral families (Polyomaviridae, Flaviviridae, Togaviridae, and Phenuiviridae) highlighted the wide diversity of these viral families, and in some cases, a potential risk of transmission to humans. All these findings provide significant insights into the diversity of rodent viruses in Amazonia, and emphasize that habitats and the host’s dietary ecology may drive viral diversity. Linking viral richness and abundance to the ecology of their hosts and their responses to habitat disturbance could be the starting point for a better understanding of viral emergence and for future management of ecosystems.
Published: 2021
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15. Hantavirus Pulmonary Syndrome Caused by Maripa Virus in French Guiana, 2008–2016

Author: Séverine Matheus, Hatem Kallel, Claire Mayence, Laetitia Bremand, Stéphanie Houcke, Dominique Rousset, Vincent Lacoste, Benoit de Thoisy, Didier Hommel, and Anne Lavergne
Subjects: hantavirus, Maripa virus, French Guiana, human cases, hantavirus pulmonary syndrome, viruses, Medicine, Infectious and parasitic diseases, RC109-216
Abstract: We report 5 human cases of hantavirus pulmonary syndrome found during surveillance in French Guiana in 2008–2016; of the 5 patients, 4 died. This pathogen should continue to be monitored in humans and rodents in effort to reduce the occurrence of these lethal infections in humans stemming from ecosystem disturbances.
Published: 2017
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16. Evidence of cryptic lineages within a small South American crocodilian: the Schneider’s dwarf caiman Paleosuchus trigonatus (Alligatoridae: Caimaninae)

Author: Pedro Senna Bittencourt, Zilca Campos, Fábio de Lima Muniz, Boris Marioni, Bruno Campos Souza, Ronis Da Silveira, Benoit de Thoisy, Tomas Hrbek, and Izeni Pires Farias
Subjects: Jacaré-coroa, Conservation genetics, Amazonian crocodilians, Biogeography, Population genetics, Diversification, Medicine, Biology (General), QH301-705.5
Abstract: Schneider’s dwarf caiman Paleosuchus trigonatus is one of the smallest living crocodilians. Due to its broad distribution, cryptic behavior, and small home range, the species is well suited for the study of phylogeographic patterns on a continental scale. Additionally, this species is under threat due to habitat loss, trade and harvest, but is considered at low conservation risk by the IUCN. In the present study we test the hypothesis that P. trigonatus is comprised of geographically structured lineages. Phylogenetic reconstructions of the mitochondrial cytochrome b gene and single locus species discovery methods revealed the existence of two well-supported lineages within P. trigonatus—an Amazonian and Guianan lineage. Fossil calibrated divergence of these lineages was estimated to have occurred in the Late Miocene (7.5 Ma). The hypothesis that the Atlantic coast drainages might have been colonized from the southeast or central Amazon is supported by demographic metrics and relatively low genetic diversity of the Coastal and upper Branco populations when compared to the Amazon basin populations. The Amazon basin lineage is structured along an east-west gradient, with a sharp transition in haplotype frequencies to the east and west of the Negro and Madeira rivers. These lineages are already under anthropogenic threat and, therefore, are conservation dependent. Recognition of these lineages will foster discussion of conservation future of P. trigonatus and these lineages.
Published: 2019
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17. Persistence of Yellow fever virus outside the Amazon Basin, causing epidemics in Southeast Brazil, from 2016 to 2018.

Author: Izabela Maurício de Rezende, Lívia Sacchetto, Érica Munhoz de Mello, Pedro Augusto Alves, Felipe Campos de Melo Iani, Talita Émile Ribeiro Adelino, Myrian Morato Duarte, Ana Luísa Furtado Cury, André Felipe Leal Bernardes, Tayrine Araújo Santos, Leonardo Soares Pereira, Maria Rita Teixeira Dutra, Dario Brock Ramalho, Benoit de Thoisy, Erna Geessien Kroon, Giliane de Souza Trindade, and Betânia Paiva Drumond
Subjects: Arctic medicine. Tropical medicine, RC955-962, Public aspects of medicine, RA1-1270
Abstract: Yellow fever (YF) is endemic in the Brazilian Amazon Basin, and sporadic outbreaks take place outside the endemic area in Brazil. Since 2016, YF epidemics have been occurring in Southeast Brazil, with more than 1,900 human cases and more than 1,600 epizooties of non-human primates (NHPs) reported until April 2018. Previous studies have demonstrated that Yellow fever virus (YFV) causing outbreaks in 2017 formed a monophyletic group.Aiming to decipher the origin of the YFV responsible for the recent epidemics, we obtained nucleotide sequences of YFV detected in humans (n = 6) and NHPs (n = 10) from Minas Gerais state during 2017-2018. Next, we performed evolutionary analyses and discussed the results in the light of epidemiological records (official numbers of YFV cases at each Brazilian Federative unit, reported by the Brazilian Ministry of Health). Nucleotide sequences of YFV from Southeast Brazil from 2016 to 2018 were highly conserved and formed a monophyletic lineage (BR-YFV_2016/18) within the genotype South America I. Different clusters were observed within lineage BR-YFV_2016/18, one containing the majority of isolates (from humans and NHPs), indicating the sylvatic transmission of YFV. We also detected a cluster characterized by two synapomorphies (amino acid substitutions) that contained YFV only associated with NHP what should be further investigated. The topology of lineage BR-YFV_2016/18 was congruent with epidemiological and temporal patterns of the ongoing epidemic. YFV isolates detected in 2016, in São Paulo state were located in the most basal position of the lineage, followed by the isolates from Minas Gerais and Espírito Santo obtained in 2017 and 2018. The most recent common ancestor of the lineage BR-YFV_2016/18 dated to 2015 (95% credible intervals = 2014-2016), in a period that was coincident with the reemergence of YFV in the Midwest region of Brazil.The results demonstrated a single introduction of YFV in the Southeast region and the silent viral circulation before the onset of the outbreaks in 2016. Evolutionary analyses combined with epidemiological records supported the idea that BR-YFV_2016/18 was probably introduced from the Midwest into the Southeast region, possibly in São Paulo state. The persistence of YFV in the Southeast region, causing epidemics from 2016 to 2018, suggests that this region presents suitable ecological and climatic conditions for YFV maintenance during the epidemic and interepidemic seasons. This fact poses risks for the establishing of YF enzootic cycles and epidemics, outside the Amazon Basin in Brazil. YF surveillance and studies of viral dynamics deserve particular attention, especially in Midwest, Southeast and neighbor regions which are the main areas historically associated with YF outbreaks outside the Amazon Basin. YFV persistence in Southeast Brazil should be carefully considered in the context of public health, especially for public health decision-makers and researchers.
Published: 2018
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18. The role of Pleistocene climate change in the genetic variability, distribution and demography of Proechimys cuvieri and P. guyannensis (Rodentia: Echimyidae) in northeastern Amazonia.

Author: Claudia Regina Silva, Camila Cherem Ribas, Maria Nazareth F Da Silva, Rafael Nascimento Leite, François Catzeflis, Duke S Rogers, and Benoit De Thoisy
Subjects: Medicine, Science
Abstract: The spiny rats, genus Proechimys, have the highest species richness within the Echimyidae family, as well as species with high genetic variability. The genus distribution includes tropical South America and Central America south to Honduras. In this study, we evaluate the phylogeographic histories of Proechimys guyannensis and P. cuvieri using cytochrome b, in a densely sampled area in northeastern Amazon where both species are found in sympatry in different environments. For each species, Bayesian and Maximum Likelihood phylogenetic analysis were congruent and recovered similar clades in the studied area. Bayesian phylogenetic analysis using a relaxed molecular clock showed that these clusters of haplotypes diversified during Pleistocene for both species. Apparently, the large rivers of the region did not act as barriers, as some clades include specimens collected from opposite banks of Oiapoque, Araguari and Jari rivers. Bayesian skyline plot analysis showed recent demographic expansion in both species. The Pleistocene climatic changes in concert with the geologic changes in the Amazon fan probably acted as drivers in the diversification that we detected in these two spiny rats. Proechimys cuvieri and P. guyannensis show genetic structure in the eastern part of the Guiana region. Greater genetic distances observed in P. guyannensis, associated with highly structured groups, suggest that more detailed studies of systematics and ecology should be directed to this species.
Published: 2018
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19. Green turtle (Chelonia mydas) genetic diversity at Paranaguá Estuarine Complex feeding grounds in Brazil

Author: Juliana Costa Jordão, Ana Cristina Vigliar Bondioli, Flavia Maria Guebert, Benoit de Thoisy, and Lurdes Foresti de Almeida Toledo
Subjects: Chelonia mydas, mtDNA, feeding grounds, mixed stock analysis, connectivity, Genetics, QH426-470
Abstract: Sea turtles are marine reptiles that undertake long migrations through their life, with limited information regarding juvenile stages. Feeding grounds (FGs), where they spend most of their lives, are composed by individuals from different natal origins, known as mixed stock populations. The aim of this study was to assess genetic composition, natal origins and demographic history of juvenile green turtles (Chelonia mydas) at the Paranaguá Estuarine Complex (PEC), Brazil, considered a Natural World Heritage site. Tissue samples of stranded animals were collected (n = 60), and 700 bp mitochondrial DNA sequences were generated and compared to shorter sequences from previously published studies. Global exact tests of differentiation revealed significant differences among PEC and the other FGs, except those at the South Atlantic Ocean. Green turtles at PEC present genetic signatures similar to those of nesting females from Ascension Island, Guinea Bissau and Aves Island/Surinam. Population expansion was evidenced to have occurred 20–25 kYA, reinforcing the hypothesis of recovery from Southern Atlantic refugia after the last Glacial Maximum. These results contribute to a better understanding of the dynamics of green turtle populations at a protected area by providing knowledge on the dispersion patterns and reinforcing the importance of the interconnectivity between nesting and foraging populations.
Published: 2015
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20. The hidden anatomy of paranasal sinuses reveals biogeographically distinct morphotypes in the nine-banded armadillo (Dasypus novemcinctus)

Author: Guillaume Billet, Lionel Hautier, Benoit de Thoisy, and Frédéric Delsuc
Subjects: Xenarthra, Skull, Mammalia, Systematics, Cingulata, Biogeography, Medicine, Biology (General), QH301-705.5
Abstract: Background With their Pan-American distribution, long-nosed armadillos (genus Dasypus) constitute an understudied model for Neotropical biogeography. This genus currently comprises seven recognized species, the nine-banded armadillo (D. novemcinctus) having the widest distribution ranging from Northern Argentina to the South-Eastern US. With their broad diversity of habitats, nine-banded armadillos provide a useful model to explore the effects of climatic and biogeographic events on morphological diversity at a continental scale. Methods Based on a sample of 136 skulls of Dasypus spp. belonging to six species, including 112 specimens identified as D. novemcinctus, we studied the diversity and pattern of variation of paranasal cavities, which were reconstructed virtually using µCT-scanning or observed through bone transparency. Results Our qualitative analyses of paranasal sinuses and recesses successfully retrieved a taxonomic differentiation between the traditional species D. kappleri, D. pilosus and D. novemcinctus but failed to recover diagnostic features between the disputed and morphologically similar D. septemcinctus and D. hybridus. Most interestingly, the high variation detected in our large sample of D. novemcinctus showed a clear geographical patterning, with the recognition of three well-separated morphotypes: one ranging from North and Central America and parts of northern South America west of the Andes, one distributed across the Amazonian Basin and central South America, and one restricted to the Guiana Shield. Discussion The question as to whether these paranasal morphotypes may represent previously unrecognized species is to be evaluated through a thorough revision of the Dasypus species complex integrating molecular and morphological data. Remarkably, our recognition of a distinct morphotype in the Guiana Shield area is congruent with the recent discovery of a divergent mitogenomic lineage in French Guiana. The inflation of the second medialmost pair of caudal frontal sinuses constitutes an unexpected morphological diagnostic feature for this potentially distinct species. Our results demonstrate the benefits of studying overlooked internal morphological structures in supposedly cryptic species revealed by molecular data. It also illustrates the under-exploited potential of the highly variable paranasal sinuses of armadillos for systematic studies.
Published: 2017
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21. Beyond the carapace: skull shape variation and morphological systematics of long-nosed armadillos (genus Dasypus)

Author: Lionel Hautier, Guillaume Billet, Benoit de Thoisy, and Frédéric Delsuc
Subjects: Dasypus, Skull, Geometric morphometrics, Cingulata, Anatomy, Species complex, Medicine, Biology (General), QH301-705.5
Abstract: Background The systematics of long-nosed armadillos (genus Dasypus) has been mainly based on a handful of external morphological characters and classical measurements. Here, we studied the pattern of morphological variation in the skull of long-nosed armadillos species, with a focus on the systematics of the widely distributed nine-banded armadillo (Dasypus novemcinctus). Methods We present the first exhaustive 3D comparison of the skull morphology within the genus Dasypus, based on micro-computed tomography. We used geometric morphometric approaches to explore the patterns of the intra- and interspecific morphological variation of the skull with regard to several factors such as taxonomy, geography, allometry, and sexual dimorphism. Results We show that the shape and size of the skull vary greatly among Dasypus species, with Dasypus pilosus representing a clear outlier compared to other long-nosed armadillos. The study of the cranial intraspecific variation in Dasypus novemcinctus evidences clear links to the geographic distribution and argues in favor of a revision of past taxonomic delimitations. Our detailed morphometric comparisons detected previously overlooked morphotypes of nine-banded armadillos, especially a very distinctive unit restricted to the Guiana Shield. Discussion As our results are congruent with recent molecular data and analyses of the structure of paranasal sinuses, we propose that Dasypus novemcinctus should be regarded either as a polytypic species (with three to four subspecies) or as a complex of several distinct species.
Published: 2017
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22. Virome analysis of two sympatric bat species (Desmodus rotundus and Molossus molossus) in French Guiana.

Author: Arielle Salmier, Sourakhata Tirera, Benoit de Thoisy, Alain Franc, Edith Darcissac, Damien Donato, Christiane Bouchier, Vincent Lacoste, and Anne Lavergne
Subjects: Medicine, Science
Abstract: Environmental disturbances in the Neotropics (e.g., deforestation, agriculture intensification, urbanization) contribute to an increasing risk of cross-species transmission of microorganisms and to disease outbreaks due to changing ecosystems of reservoir hosts. Although Amazonia encompasses the greatest diversity of reservoir species, the outsized viral population diversity (virome) has yet to be investigated. Here, through a metagenomic approach, we identified 10,991 viral sequences in the saliva and feces of two bat species, Desmodus rotundus (hematophagous), trapped in two different caves surrounded by primary lowland forest, and Molossus molossus (insectivorous), trapped in forest and urban habitats. These sequences are related to 51 viral families known to infect a wide range of hosts (i.e., bacteria, plants, insects and vertebrates). Most viruses detected reflected the diet of bat species, with a high proportion of plant and insect-related viral families for M. molossus and a high proportion of vertebrate-related viral families for D. rotundus, highlighting its influence in shaping the viral diversity of bats. Lastly, we reconstructed the phylogenetic relationships for five vertebrate-related viral families (Nairoviridae, Circoviridae, Retroviridae, Herpesviridae, Papillomaviridae). The results showed highly supported clustering with other viral sequences of the same viral family hosted by other bat species, highlighting the potential association of viral diversity with the host's diet. These findings provide significant insight into viral bat diversity in French Guiana belonging to the Amazonian biome and emphasize that habitats and the host's dietary ecology may drive the viral diversity in the bat communities investigated.
Published: 2017
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23. Predators, Prey and Habitat Structure: Can Key Conservation Areas and Early Signs of Population Collapse Be Detected in Neotropical Forests?

Author: Benoit de Thoisy, Ibrahim Fayad, Luc Clément, Sébastien Barrioz, Eddy Poirier, and Valéry Gond
Subjects: Medicine, Science
Abstract: Tropical forests with a low human population and absence of large-scale deforestation provide unique opportunities to study successful conservation strategies, which should be based on adequate monitoring tools. This study explored the conservation status of a large predator, the jaguar, considered an indicator of the maintenance of how well ecological processes are maintained. We implemented an original integrative approach, exploring successive ecosystem status proxies, from habitats and responses to threats of predators and their prey, to canopy structure and forest biomass. Niche modeling allowed identification of more suitable habitats, significantly related to canopy height and forest biomass. Capture/recapture methods showed that jaguar density was higher in habitats identified as more suitable by the niche model. Surveys of ungulates, large rodents and birds also showed higher density where jaguars were more abundant. Although jaguar density does not allow early detection of overall vertebrate community collapse, a decrease in the abundance of large terrestrial birds was noted as good first evidence of disturbance. The most promising tool comes from easily acquired LiDAR data and radar images: a decrease in canopy roughness was closely associated with the disturbance of forests and associated decreasing vertebrate biomass. This mixed approach, focusing on an apex predator, ecological modeling and remote-sensing information, not only helps detect early population declines in large mammals, but is also useful to discuss the relevance of large predators as indicators and the efficiency of conservation measures. It can also be easily extrapolated and adapted in a timely manner, since important open-source data are increasingly available and relevant for large-scale and real-time monitoring of biodiversity.
Published: 2016
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24. Bioecological Drivers of Rabies Virus Circulation in a Neotropical Bat Community.

Author: Benoit de Thoisy, Hervé Bourhy, Marguerite Delaval, Dominique Pontier, Laurent Dacheux, Edith Darcissac, Damien Donato, Amandine Guidez, Florence Larrous, Rachel Lavenir, Arielle Salmier, Vincent Lacoste, and Anne Lavergne
Subjects: Arctic medicine. Tropical medicine, RC955-962, Public aspects of medicine, RA1-1270
Abstract: INTRODUCTION:In addition to the commonly accepted importance of the vampire bat in the maintenance and transmission of the rabies virus (RABV) in South America, RABV infection of other species is widely evidenced, challenging their role in the viral cycle. METHODOLOGY / PRINCIPLES FINDINGS:To identify the bioecological drivers of RABV circulation in neotropical bat communities, we conducted a molecular and serological survey on almost 1,000 bats from 30 species, and a 4-year longitudinal survey in two colonies of vampire bats in French Guiana. RABV was molecularly detected in a common vampire and in a frugivorous bat. The sequences corresponded to haematophagous bat-related strains and were close to viruses circulating in the Brazilian Amazon region. Species' seroprevalence ranged from 0 to 20%, and the risk of seropositivity was higher in bats with a haematophagous diet, living in monospecific colonies and in dense forests. The longitudinal survey showed substantial temporal fluctuations, with individual waves of seroconversions and waning immunity. The high prevalences observed in bat communities, in most habitats and in species that do not share the same microhabitats and bioecological patterns, the temporal variations, and a rather short period of detectable antibodies as observed in recaptured vampires suggest (i) frequent exposure of animals, (ii) an ability of the infected host to control and eliminate the virus, (iii) more relaxed modes of exposure between bats than the commonly assumed infection via direct contact with saliva of infected animals, all of which should be further investigated. CONCLUSIONS / SIGNIFICANCE:We hypothesize that RABV circulation in French Guiana is mainly maintained in the pristine forest habitats that may provide sufficient food resources to allow vampire bats, the main prevalent species, to survive and RABV to be propagated. However, on the forest edge and in disturbed areas, human activities may induce more insidious effects such as defaunation. One of the ecological consequences is the disappearance of resources for tertiary or secondary consumers. Populations of vampires may then shift to alternative resources such as cattle, domestic animals and humans. Therefore, a good forest status, allowing both a dilution effect in highly rich bat communities and the maintenance of large populations of medium-sized and large mammals used as prey by vampires, should prevent their migration to anthropized areas.
Published: 2016
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25. Population genetic analysis of Caiman crocodilus (Linnaeus, 1758) from South America

Author: William R. Vasconcelos, Tomas Hrbek, Ronis da Silveira, Benoit de Thoisy, Boris Marioni, and Izeni P. Farias
Subjects: genetic structure, phylogeography, genetic diversity, demographic expansion, cytochrome b, Caiman crocodilus, Genetics, QH426-470
Abstract: The genetic structure of Caiman crocodilus was investigated using a 1085 bp mtDNA fragment of the cytochrome b gene. Inferences were based on 125 individuals from nine localities in Peru, Brazil and French Guiana. With the exception of Mamirauá Lake, Anavilhanas Archipelago and the Tapará Community which show a signal of demographic expansion, the sampled localities are in a mutation-drift genetic equilibrium. Divergence between the Amazon basin and extra-Amazon basin localities is significant; however, inference from Nested Clade Analysis cannot distinguish between continuous range expansion, long distance colonization or past fragmentation; however, past fragmentation is unlikely due to low number of mutational steps separating these two regions. The divergence is probably maintained by the reduced ability of C. crocodilus to cross salt water barriers. Within the Amazon basin, continuous range expansion without isolation-by-distance is the most likely process causing genetic structuring. The observed genetic patterns are compatible with the ecology of C. crocodilus, and history of human exploitation. As commercial hunting depleted more valuable species, C. crocodilus expanded its range and ecological niche, prompting hunters to harvest it. Following a period of intense hunting, C. crocodilus is now experiencing recovery and a second population expansion especially in protected areas.
Published: 2006
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26. A hybrid swarm of manatees along the Guianas coastline, a peculiar environment under the influence of the Amazon River plume

Author: CAMILLA S. LIMA, RAFAEL F. MAGALHÃES, MIRIAM MARMONTEL, ANA CAROLINA MEIRELLES, VITOR LUZ CARVALHO, ANNE LAVERGNE, BENOIT DE THOISY, and FABRÍCIO R. SANTOS
Subjects: Conservation Genetics, Hybrid zone, Introgression, Amazon River plume, Guianas coastline, Trichechus, Science
Abstract: Abstract: The West Indian (Trichechus manatus) and Amazonian (T. inunguis) manatees have a sympatric occurrence at the mouth of the Amazon River. A result of this interspecific encounter is the occurrence of hybrids, which are frequently found along the coasts of Amapá state in Brazil, French Guiana and Guyana. Here we present new genetic evidence indicating the occurrence of a hybrid swarm along the Guianas Shield coastline, which is an interspecific hybrid zone that also separates T. manatus populations located east (Brazil) and west (Caribbean, Gulf of Mexico, Florida and Antilles). In addition, we suggest that this hybrid population occupies a peculiar mangrove-rich environment under strong influence of the Amazon River plume, which requires an independent management and should be considered a special conservation area.
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27. G lobal phylogeography of ridley sea turtles (Lepidochelys spp.):evolution, demography, connectivity, and conservation

Author: Sibelle Torres Vilaça, Anelise Torres Hahn, Eugenia Naro-Maciel, F. Alberto Abreu-Grobois, Brian W. Bowen, Jaqueline C. Castilhos, Claudio Ciofi, Nancy N. FitzSimmons, Michael P. Jensen, Angela Formia, Colin J. Limpus, Chiara Natali, Luciano S. Soares, Benoit de Thoisy, Scott D. Whiting, and Sandro L. Bonatto
Subjects: Effective population size, Marine conservation, Genetics, mtDNA control region, Microsatellites, Population structure, Marine turtle, Ecology, Evolution, Behavior and Systematics, Demographic change
Abstract: Globally distributed marine taxa are well suited for investigations of biogeographic impacts on genetic diversity, connectivity, and population demography. The sea turtle genus Lepidochelys includes the wide-ranging and abundant olive ridley (L. olivacea), and the geographically restricted and ‘Critically Endangered’ Kemp’s ridley (L. kempii). To investigate their historical biogeography, we analyzed a large dataset of mitochondrial DNA (mtDNA) sequences from olive (n = 943) and Kemp’s (n = 287) ridleys, and genotyped 15 nuclear microsatellite loci in a global sample of olive ridleys (n = 285). We found that the ridley species split ~ 7.5 million years ago, before the Panama Isthmus closure. The most ancient mitochondrial olive ridley lineage, located in the Indian Ocean, was dated to ~ 2.2 Mya. Both mitochondrial and nuclear markers revealed significant structure for olive ridleys between Atlantic (ATL), East Pacific (EP), and Indo-West Pacific (IWP) areas. However, the divergence of mtDNA clades was very recent (
Published: 2022

28. Ecology, evolution, and epidemiology of zoonotic and vector-borne infectious diseases in French Guiana: Transdisciplinarity does matter to tackle new emerging threats

Author: Anne Lavergne, Marine Ginouves, Florian Binetruy, Claude Flamand, Mathieu Nacher, Emmanuel Roux, Roxane Schaub, Sébastien Gourbière, Benoit de Thoisy, Pierre Couppié, Arthur Kocher, Lise Musset, Philippe Quénel, Sourakhata Tirera, Luisiane Carvalho, Jérôme Murienne, Sébastien Briolant, Magalie Demar, Yanouk Epelboin, Ghislaine Prévot, Olivier Duron, Isabelle Dusfour, Benjamin Roche, Maylis Douine, Stéphane Pelleau, Luana Mathieu, Agathe Chavy, Loïc Epelboin, Alain Franc, Paul Le Turnier, Pauline Thill, Jean-François Guégan, Emeline Houël, Dominique Rousset, Stanislas Talaga, Laboratoire des Interactions Virus-Hôtes [Cayenne, Guyane Française], Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Réseau International des Instituts Pasteur (RIIP), Centre de Recherche en Ecologie et Evolution de la Santé (CREES), Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Centre National de Référence du Paludisme [Cayenne, Guyane française] (CNR - laboratoire associé), Centre Collaborateur OMS pour la surveillance de la résistance aux antipaludiques [Cayenne, Guyane française] (CCOMS), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Laboratoire de Parasitologie [Cayenne, Guyane française], Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), École des Hautes Études en Santé Publique [EHESP] (EHESP), Centre de Recherches Ecologiques et Evolutives sur le Cancer (MIVEGEC-CREEC), Processus Écologiques et Évolutifs au sein des Communautés (PEEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Institut de Recherche Biomédicale des Armées [Antenne Marseille] (IRBA), Santé publique France Guyane, Santé publique France - French National Public Health Agency [Saint-Maurice, France], Université de Guyane (UG), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Centre d'investigation clinique Antilles-Guyane (CIC - Antilles Guyane), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -CHU de la Martinique [Fort de France]-Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Département de Santé Globale - Department Global Health, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Vectopôle Amazonien Emile Abonnenc [Cayenne, Guyane française], Unité d'Epidémiologie [Cayenne, Guyane française], Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), from patterns to models in computational biodiversity and biotechnology (PLEIADE), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biome Tropical et Immuno-Pathophysiologie = Tropical Biome and ImmunoPhysiopathology [Lille] (TBIP), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS)-Université de Guyane (UG), Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Max Planck Institute for the Science of Human History (MPI-SHH), Max-Planck-Gesellschaft, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre d’Investigation Clinique de Nantes (CIC Nantes), Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre hospitalier universitaire de Nantes (CHU Nantes), Centre hospitalier universitaire de Nantes (CHU Nantes), Malaria : parasites et hôtes - Malaria : parasites and hosts, Institut Pasteur [Paris] (IP), UMR 228 Espace-Dev, Espace pour le développement, Institut de Recherche pour le Développement (IRD)-Université de Perpignan Via Domitia (UPVD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM)-Université de Guyane (UG)-Université des Antilles (UA), LMI Sentinela [Rio de Janeiro], Institut de Recherche pour le Développement (IRD)-Universidade de Brasilia [Brasília] (UnB)-Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Service Universitaire des Maladies Infectieuses et du Voyageur [Tourcoing], Centre Hospitalier Tourcoing, Centre Hospitalier Gustave Dron [Tourcoing], Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), This work has benefited from three 'Investissement d’Avenir' grants managed by Agence Nationale de la Recherche (CEBA: ANR-10-LABX-25-01, TULIP: ANR-10-LABX-0041, DRIIHM: ANR-11-LABX-0010). The two lead coauthors received European funding through the European Regional Development Fund Operational Program FEDER RESERVOIRS Project (BdT) and a US NSF-NIH (NSF#1911457) Ecology of infectious diseases award (J-FG). J-FG is also supported by IRD, INRAE, and Université of Montpellier. OD thanks l’Office français de la biodiversité, le Groupe d'Étude et de Protection des Oiseaux en Guyane (GEPOG), la Direction de l'Alimentation, de l'Agriculture et de la Forêt de Guyane (DAAF). AL acknowledges European funding through the European Regional Development Fund Operational Program FEDER RESERVOIRS, CAROLLIA, EFAG and VIRUSES projects. LM is supported by European funding through the European Regional Development Fund Operational Program FEDER ELIMALAR project and Santé publique France as the National Reference Center for Malaria. PQ thanks Publique France/Cire Guyane, CNR sur les arboviroses, CNR du paludisme. EH and ID acknowledge European funding through the European Regional Development Fund Operational Program FEDER CONTROLE Projet, the French Guiana Regional Council and the Air Liquide Foundation. SB is supported by the French Army (Grant LR607e). ER is grateful for European funding through the European Regional Development Fund Operational Program FEDER OSE-Guyamapa project, the French Embassy in Brazil, the Guyamazon program ('GAPAM-Sentinela' project), CNES, and the Bill and Melinda Gates Foundation., ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-11-LABX-0010,DRIIHM / IRDHEI,Dispositif de recherche interdisciplinaire sur les Interactions Hommes-Milieux(2011), Génétique et évolution des maladies infectieuses (GEMI), Centre National de Référence du Paludisme [Cayenne, Guyane française] (CNR), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Génétique et évolution des maladies infectieuses (GEMI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Universidade de Brasilia [Brasília] (UnB)-Fundação Oswaldo Cruz (FIOCRUZ), Dusfour, Isabelle, Laboratoires d'excellence - CEnter of the study of Biodiversity in Amazonia - - CEBA2010 - ANR-10-LABX-0025 - LABX - VALID, Towards a Unified theory of biotic Interactions: the roLe of environmental - - TULIP2010 - ANR-10-LABX-0041 - LABX - VALID, Dispositif de recherche interdisciplinaire sur les Interactions Hommes-Milieux - - DRIIHM / IRDHEI2011 - ANR-11-LABX-0010 - LABX - VALID, Université d'Angers (UA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU de la Martinique [Fort de France]-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Institut Pasteur [Paris], Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Université de Guyane (UG), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université de Guyane (UG)-Université des Antilles (UA)-Institut de Recherche pour le Développement (IRD)-Université de Perpignan Via Domitia (UPVD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Santé et de la Recherche Médicale (INSERM)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université d'Angers (UA)
Subjects: 0301 basic medicine, Microbiology (medical), Emerging and reemerging infectious diseases, Ecology (disciplines), media_common.quotation_subject, [SDV]Life Sciences [q-bio], [SDE.MCG]Environmental Sciences/Global Changes, 030106 microbiology, Immigration, Interdisciplinary Research, Wildlife, Vector Borne Diseases, Animals, Wild, Anthropogenic pressures, Biology, Microbiology, 03 medical and health sciences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Zoonoses, Genetics, Prevalence, Animals, Humans, Human Activities, Molecular Biology, Epidemiologic transition, Global change, Ecology, Evolution, Behavior and Systematics, Ecosystem, media_common, Demography, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Resistance (ecology), Ecology, Incidence, Outbreak, 15. Life on land, French Guiana, [SDV] Life Sciences [q-bio], Epidemiological transition, [SDE.MCG] Environmental Sciences/Global Changes, 030104 developmental biology, Infectious Diseases, Promiscuity, Vector (epidemiology), [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases
Abstract: International audience; French Guiana is a European ultraperipheric region located on the northern Atlantic coast of South America. It constitutes an important forested region for biological conservation in the Neotropics. Although very sparsely populated, with its inhabitants mainly concentrated on the Atlantic coastal strip and along the two main rivers, it is marked by the presence and development of old and new epidemic disease outbreaks, both research and health priorities. In this review paper, we synthetize 15 years of multidisciplinary and integrative research at the interface between wildlife, ecosystem modification, human activities and sociodemographic development, and human health. This study reveals a complex epidemiological landscape marked by important transitional changes, facilitated by increased interconnections between wildlife, land-use change and human occupation and activity, human and trade transportation, demography with substantial immigration, and identified vector and parasite pharmacological resistance. Among other French Guianese characteristics, we demonstrate herein the existence of more complex multi-host disease life cycles than previously described for several disease systems in Central and South America, which clearly indicates that today the greater promiscuity between wildlife and humans due to demographic and economic pressures may offer novel settings for microbes and their hosts to circulate and spread. French Guiana is a microcosm that crystallizes all the current global environmental, demographic and socioeconomic change conditions, which may favor the development of ancient and future infectious diseases.
Published: 2021

29. The influence of habitat on viral diversity in neotropical rodent hosts

Author: Anne Lavergne, Damien Donato, Alain Franc, Sourakhata Tirera, Benoit de Thoisy, Christiane Bouchier, Vincent Lacoste, Laboratoire des Interactions Virus-Hôtes [Cayenne, Guyane Française], Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Institut Pasteur [Paris], Département de Virologie - Department of Virology, Arbovirus & Emerging Viral Diseases [Vientiane] (A&EVD), Institut Pasteur du Laos, Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), from patterns to models in computational biodiversity and biotechnology (PLEIADE), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), S. Tirera was funded by the RESERVOIRS program, supported by European funds (PO FSE 2014-2020), an 'Investissement d’Avenir' grant managed by the Agence Nationale de la Recherche (CEBA, ref. ANR-10-LABX-25-01), a European Commission 'REGPOT-CT-2011-285837-STRonGer' grant within the FP7, and the Institut Pasteur de la Guyane. This study was conducted within the 'BioViRo' program, supported by an 'Investissement d’Avenir' grant managed by the Agence Nationale de la Recherche (CEBA, reference ANR-10-LABX-25-01). Field work conducted by BdT was funded by the ViRUSES program, supported by European funds (FEDER) and assistance from Région Guyane and Direction Régionale pour la Recherche et la Technologie, the ZNIEFF Guyane (DEAL Guyane) program, the GUYAMAZON II program, and Réseau des Observatoires Hommes-Milieux (OHM-Oyapok APR 2013, François Catzeflis). High-throughput sequencing was performed on the Biomics Platform, C2RT, Institut Pasteur, Paris, France, supported by France Génomique (ANR-10-INBS-09-09) and IBISA., ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), European Project: 285837,EC:FP7:REGPOT,FP7-REGPOT-2011-1,STRONGER(2011), Institut Pasteur [Paris] (IP), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), and Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest
Subjects: Viral ecology, Ecology (disciplines), viruses, Rodentia, Forests, Biology, Microbiology, Rodents, Article, Viral phylogenies, 03 medical and health sciences, Amazonia, Abundance (ecology), Zoonoses, Virology, Animals, Human virome, Alpha diversity, Ecosystem, Phylogeny, 030304 developmental biology, 0303 health sciences, Ecology, 030306 microbiology, Host (biology), Virome, Genetic Variation, 15. Life on land, QR1-502, 3. Good health, Infectious Diseases, Habitat, Metagenomics, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDE]Environmental Sciences, Metagenome, Species richness
Abstract: Rodents are important reservoirs of numerous viruses, some of which have significant impacts on public health. Ecosystem disturbances and decreased host species richness have been associated with the emergence of zoonotic diseases. In this study, we aimed at (a) characterizing the viral diversity in seven neotropical rodent species living in four types of habitats and (b) exploring how the extent of environmental disturbance influences this diversity. Through a metagenomic approach, we identified 77,767 viral sequences from spleen, kidney, and serum samples. These viral sequences were attributed to 27 viral families known to infect vertebrates, invertebrates, plants, and amoeba. Viral diversities were greater in pristine habitats compared with disturbed ones, and lowest in peri-urban areas. High viral richness was observed in savannah areas. Differences in these diversities were explained by rare viruses that were generally more frequent in pristine forest and savannah habitats. Moreover, changes in the ecology and behavior of rodent hosts, in a given habitat, such as modifications to the diet in disturbed vs. pristine forests, are major determinants of viral composition. Lastly, the phylogenetic relationships of four vertebrate-related viral families (Polyomaviridae, Flaviviridae, Togaviridae, and Phenuiviridae) highlighted the wide diversity of these viral families, and in some cases, a potential risk of transmission to humans. All these findings provide significant insights into the diversity of rodent viruses in Amazonia, and emphasize that habitats and the host’s dietary ecology may drive viral diversity. Linking viral richness and abundance to the ecology of their hosts and their responses to habitat disturbance could be the starting point for a better understanding of viral emergence and for future management of ecosystems.
Published: 2021

30. Paramyxovirus circulation in bat species from French Guiana

Author: Vincent Lacoste, Damien Donato, Anne Lavergne, Edith Darcissac, Benoit de Thoisy, Laboratoire des Interactions Virus-Hôtes [Cayenne, Guyane Française], Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Réseau International des Instituts Pasteur (RIIP), Département de Virologie - Department of Virology, Institut Pasteur [Paris] (IP), This study was funded by the CAROLIA and RESERVOIRS programs supported by European Funds (ERDF/FEDER), the Région Guyane and the Direction Régionale pour la Recherche et la Technologie. It also received 'Investissement d'Avenir' grants managed by the Agence Nationale de la Recherche (CEBA, Ref. ANR-10-LABX-25-01)., and ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010)
Subjects: 0301 basic medicine, Microbiology (medical), animal structures, Highly pathogenic, viruses, 030106 microbiology, Zoology, Cross-species transmission, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Mormoopidae, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Microbiology, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Genus, Chiroptera, Pteronotus, Bats, Genetics, Animals, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Carollia perspicillata, Paramyxoviridae Infections, biology, Phylogenetic tree, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], biochemical phenomena, metabolism, and nutrition, biology.organism_classification, French Guiana, 030104 developmental biology, Infectious Diseases, Paramyxoviridae, Paramyxoviruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Desmodus rotundus, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Phylogenetic relationships, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; Bats are recognized as reservoirs of numerous viruses. Among them, paramyxoviruses, for example, Hendra and Nipah viruses, are highly pathogenic to humans. Nothing is known regarding the circulation of this viral family in bats from French Guiana. To search for the presence of paramyxoviruses in this territory, 103 bats of seven different species were sampled and screened using a molecular approach. Four distinct paramyxovirus sequences were detected from three bat species (Desmodus rotundus, Carollia perspicillata, and Pteronotus alitonus) at high prevalence rates. In D. rotundus, two types of paramyxovirus cocirculate, with most of the bats co-infected. The phylogenetic analysis of these sequences revealed that three of them were closely related to previously characterized sequences from D. rotundus, C. perspicillata, and P. parnellii from Brazil and Costa Rica. The fourth sequence, identified in D. rotundus, was closely related to the one detected in P. alitonus in French Guiana and to previously described sequences detected in P. parnellii in Costa Rica. All paramyxovirus sequences detected in this study are close to the Jeilongvirus genus. Altogether, our results and those of previous studies indicate a wide geographical distribution of these paramyxoviruses (from Central to South America) and suggest potential cross-species transmissions of paramyxoviruses between two different bat families: Mormoopidae (P. alitonus) and Phyllostomidae (D. rotundus). In addition, their closeness to paramyxoviruses identified in rodents emphasizes the need to investigate the role of these animals as potential reservoirs or incidental hosts. Finally, the high prevalence rates of some paramyxoviruses in certain bat species, associated with the presence of large bat colonies and, in some cases, their potential proximity with humans are all parameters that can contribute to the risk of cross-species transmission between bat species and to the emergence of new paramyxoviruses in humans, a risk that deserves further investigation.
Published: 2021

31. Designation of a neotype for mazama americana (Artiodactyla, cervidae) reveals a cryptic new complex of brocket deer species

Author: José Maurício Barbanti Duarte, Benoit de Thoisy, Aline Meira Bonfim Mantellatto, Jorge Alfonso Morales-Donoso, Eluzai Dinai Pinto Sandoval, Iara Maluf Tomazella, Analorena Cifuentes-Rincón, Universidade Estadual Paulista (Unesp), Universidade Federal do Sul da Bahia, and Kwata NGO
Subjects: 0106 biological sciences, 0301 basic medicine, Morphology, chromosomes, Species complex, topotype, Topotype, Biodiversity, Zoology, Morphology (biology), mitochondrial DNA, Biology, 010603 evolutionary biology, 01 natural sciences, cytogenetics, red brocket deer, Chromosomes, 03 medical and health sciences, Cytogenetics, Red brocket deer, Genus, Mazama americana, biodiversity chromosomes cytogenetics French Guiana mitochondrial DNA morphology red brocket deer topotype, morphology, lcsh:Zoology, Animalia, lcsh:QL1-991, Brocket deer, Chordata, Ecology, Evolution, Behavior and Systematics, biodiversity, Artiodactyla, Cervidae, Red brocket, biology.organism_classification, Mitochondrial DNA, French Guiana, 030104 developmental biology, Taxon, Mazama, Mammalia, Animal Science and Zoology, Type locality
Abstract: Made available in DSpace on 2020-12-12T02:48:04Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-01-01 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Mazama americana (red brocket deer) is the genus-type species (first species described for this genus) and the basis for the identity of other Mazama species. Mazama americana is one of the most abundant and widely distributed deer species in the neotropical forest. However, recent studies suggest that this taxon belongs to a species complex. Our goal was to collect an animal at the type locality (topotype) in French Guiana with the aim of characterizing the morphological (biometric, craniometric), cytogenetic (Giemsa, C-banding, G-banding and NOR) and molecular (mitochondrial DNA) features. The compari-sons showed that the collected specimen was very similar morphologically to specimens from other South American populations, but it was cytogenetically and molecularly very different from any of the cytotypes already described for this species, corroborating the existence of a complex of cryptic species. The data suggest that the M. americana topotype is a different species from all the cytotypes already described in the literature and which occupy the southern region of the Amazon River. The characterization and designation of the M. americana neotype is the first step toward a taxonomic reorganization of the genus Mazama, with the potential identification of new species. Núcleo de Pesquisa e Conservação de Cervídeos (NUPECCE) Faculdade de Ciências Agrárias e Veterinárias da Universidade Estadual Paulista (UNESP), Via de Acesso Paulo Donato Castellane, s/n Universidade Federal do Sul da Bahia Campus Sosígenes Costa Kwata NGO, 16 Avenue Pasteur Núcleo de Pesquisa e Conservação de Cervídeos (NUPECCE) Faculdade de Ciências Agrárias e Veterinárias da Universidade Estadual Paulista (UNESP), Via de Acesso Paulo Donato Castellane, s/n
Published: 2020

32. The Amazonian Savannas of French Guiana: Cultural and Social Importance, Biodiversity, and Conservation Challenges

Author: Olivier Claessens, Karen Mustin, Stéphen Rostain, Maël Dewynter, Doyle McKey, Benoit de Thoisy, Marianne Palisse, William Douglas de Carvalho, François Catzeflis, Anna Stier, Universidade Federal do Amapà (UNIFAP), Archéologie des Amériques (ArchAm), Université Paris 1 Panthéon-Sorbonne (UP1)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), University of Aberdeen, Universidade Federal de Pelotas = Federal University of Pelotas (UFPel), Laboratoire Ecologie, Evolution, Interactions des Systèmes amazoniens (LEEISA), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS), Université Panthéon-Sorbonne (UP1)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Laboratoire Ecologie, évolution, interactions des systèmes amazoniens (LEEISA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut de Recherche pour le Développement (IRD [France-Sud])
Subjects: 0106 biological sciences, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Amazonian, Biodiversity, Endangered species, Colonialism, 010603 evolutionary biology, 01 natural sciences, Invasive species, Nature and Landscape Conservation, biodiversity, Ecology, Fire regime, business.industry, Agroforestry, 010604 marine biology & hydrobiology, conservation, 15. Life on land, [SHS.ANTHRO-SE]Humanities and Social Sciences/Social Anthropology and ethnology, [SDE.ES]Environmental Sciences/Environmental and Society, savanna, French Guiana, Geography, archeology, 13. Climate action, Agriculture, [SHS.ENVIR]Humanities and Social Sciences/Environmental studies, Threatened species, socioecological systems, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business
Abstract: International audience; The Amazonian savannas of French Guiana are rare and of high ecological and cultural value but are also highly threatened. They are socioecological systems that have been coconstructed by humans and nature and today form mosaic landscapes along the country's coast. From pre-Columbian raised fields through colonial and Cr eole uses to contemporary uses, they have been largely shaped and modified by human activities. They are currently threatened by changes in fire regimes, agricultural practices, invasive species, and infrastructure development. Less than 3% are protected, despite their importance for several endangered animal and plant species. A shift is required in the way we think about their conservation to create a new strategy that would be completely different from existing French environmental protection tools and adapted to the complexity of these landscapes.
Published: 2020

33. Forests and emerging infectious diseases: Unleashing the beast within

Author: Julien Cappelle, Jean-François Guégan, Ahidjo Ayouba, Benoit de Thoisy, Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Comité National Francais Changements Globaux (CNFCG), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Recherches Translationnelles sur le VIH et les maladies infectieuses (TransVIHMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 1 (UM1)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Universtié Yaoundé 1 [Cameroun]-Université de Montpellier (UM), Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Laboratoire des Interactions Virus-Hôtes [Cayenne, Guyane Française], Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), ANR-10-LABX-25-01/10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), Génétique et évolution des maladies infectieuses (GEMI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), Mivegec, HAL, Laboratoires d'excellence - CEnter of the study of Biodiversity in Amazonia - - CEBA2010 - ANR-10-LABX-0025 - LABX - VALID, Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), and Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)
Subjects: 010504 meteorology & atmospheric sciences, IMPACT, [SDV]Life Sciences [q-bio], Biodiversity, 010501 environmental sciences, L73 - Maladies des animaux, 01 natural sciences, Ecosystem services, K01 - Foresterie - Considérations générales, [SDV.EE.ECO] Life Sciences [q-bio]/Ecology, environment/Ecosystems, human pathogen, General Environmental Science, disease transmission, environmental impacts, NIPAH VIRUS, Geography, Systematic review, BIODIVERSITY LOSS, GLOBAL TRENDS, HOST-RANGE, ecology, Infection risk, environmental impacts KeyWords Plus:LAND-USE CHANGE, Agent pathogène, emerging infectious diseases, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, MALARIA, Deforestation, Ecosystem, Forest clearing, ZONE FORESTIERE, Environmental planning, Transmission des maladies, 0105 earth and related environmental sciences, forests, ZOONOTIC DISEASE, Renewable Energy, Sustainability and the Environment, Public Health, Environmental and Occupational Health, Impact sur l'environnement, 15. Life on land, Déboisement, TOXOPLASMA-GONDII, 13. Climate action, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Maladie infectieuse, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, DEFORESTATION, Nexus (standard)
Abstract: Deforestation and associated changing landscapes are major components of environmental changes, with important implications for ecosystem functioning and biodiversity conservation. Tropical forests are hot spots of biodiversity and provide multiple goods and ecosystem services which benefit people in many ways. Forests also play an important role in health-related legends, myths, and fairy tales from all over the world, and are important sources of new potential emerging microbial threats to humans. Although plausibly numerous abundant microbial forms with a forest origin may exist, our systematic literature review shows that forest-derived infection studies are relatively unexplored, and both taxonomically and geographically biased. Since biodiversity has been associated with emergence of novel infectious diseases at macro-scale, we describe the main biogeographical patterns in the emerging infection-biodiversity-forest loss nexus. Then, we illustrate four fine-scale case studies to decipher the underlying processes of increased infection risk in changing forest clearing landscapes. Finally, we identify scientific challenges and regional management measures required to mitigate these important new emerging threats.
Published: 2020

34. Manatee genomics supports a special conservation area in the Guianas coastline under the influence of the Amazon River plume

Author: Benoit de Thoisy, Camilla S. Lima, Camila J. Mazzoni, Fabrício R. Santos, and Sibelle T. Vilaça
Subjects: geography, education.field_of_study, geography.geographical_feature_category, biology, Amazon rainforest, Population, Trichechus manatus, biology.organism_classification, Oceanography, Habitat, Trichechus inunguis, biology.animal, Manatee, River mouth, Amazonian manatee, education
Abstract: The West Indian manatee (Trichechus manatus) occurs along the Atlantic coastline and adjacent freshwater systems of South, Central and North America, from Alagoas (Brazil) to Florida (USA) and Greater Antilles. The Amazonian manatee (Trichechus inunguis) is the only Sirenian adapted exclusively to freshwater and endemic to the Amazon River basin. Previous studies have reported hybrids between T. inunguis and T. manatus close to the mouth of the Amazon River, composing a likely extensive hybrid zone along the Guianas coast of South America under the influence of the Amazon River plume. We have used ddRAD SNP data, and sequences of nuclear and mtDNA loci to characterize the genomic composition of manatees along the French Guiana coastline. We found this population to be formed by introgressed or later generation interspecific hybrids, and also describe the first T. inunguis found outside the Amazon River basin. Our results indicate that T. inunguis can survive in the Amazon River plume and have colonized independent water streams of the Guianas coastline where they likely hybridize with T. manatus. This hypothesis offers a plausible explanation for the known extension of the hybrid zone between the two species along the Guianas coastline. It also reinforces the importance of the Amazon plume, which flows westwards to the Guianas coastline and favors the dispersion of the freshwater species. This habitat functions as a large estuary-like system that provides an ecological continuum from Amazon River mouth to the disconnected waterflows of the Guianas, which deserves a status of special conservation area.
Published: 2019
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35. Evidence of cryptic lineages within a small South American crocodilian: The Schneider's dwarf caiman Paleosuchus trigonatus (Alligatoridae: Caimaninae)

Author: Zilca Campos, Ronis Da Silveira, Bruno Campos Souza, Boris Marioni, Pedro Senna Bittencourt, F. Muniz, Izeni Pires Farias, Tomas Hrbek, and Benoit de Thoisy
Subjects: 0106 biological sciences, Conservation genetics, Amazonian crocodilians, Population genetics, Lineage (evolution), lcsh:Medicine, Genomic Dna, Structure Analysis, Crocodilian, 01 natural sciences, Polymerase Chain Reaction, Phylogenetic Tree, Haplotype, Alligatoridae, IUCN Red List, Cluster Analysis, Phylogeny, Population Structure, Cryptic (era), 0303 health sciences, biology, Amazon rainforest, Ecology, General Neuroscience, Fossil, General Medicine, Biodiversity, Jacaré-coroa, Evolutionary Studies, Phylogeography, Biogeography, Genetic Variability, Diversification, Genetic Parameters, General Agricultural and Biological Sciences, Gene Structures, Principal Coordinate Analysis, Gene Flow, Gene Sequence, Maximum Likelihood Method, 010603 evolutionary biology, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Population Genetic Structure, Dna Extraction, Paleosuchus trigonatus, Genetics, Population Growth, 030304 developmental biology, Population Biology, Whole Genome Sequencing, lcsh:R, Cytochrome B, South America, biology.organism_classification, Nonhuman
Abstract: Schneider’s dwarf caimanPaleosuchus trigonatusis one of the smallest living crocodilians. Due to its broad distribution, cryptic behavior, and small home range, the species is well suited for the study of phylogeographic patterns on a continental scale. Additionally, this species is under threat due to habitat loss, trade and harvest, but is considered at low conservation risk by the IUCN. In the present study we test the hypothesis thatP. trigonatusis comprised of geographically structured lineages. Phylogenetic reconstructions of the mitochondrial cytochrome b gene and single locus species discovery methods revealed the existence of two well-supported lineages withinP. trigonatus—an Amazonian and Guianan lineage. Fossil calibrated divergence of these lineages was estimated to have occurred in the Late Miocene (7.5 Ma). The hypothesis that the Atlantic coast drainages might have been colonized from the southeast or central Amazon is supported by demographic metrics and relatively low genetic diversity of the Coastal and upper Branco populations when compared to the Amazon basin populations. The Amazon basin lineage is structured along an east-west gradient, with a sharp transition in haplotype frequencies to the east and west of the Negro and Madeira rivers. These lineages are already under anthropogenic threat and, therefore, are conservation dependent. Recognition of these lineages will foster discussion of conservation future ofP. trigonatusand these lineages.
Published: 2019

36. Virulence of atypical Toxoplasma gondii strains isolated in French Guiana in a murine model

Author: Magalie Demar, Aurélien Mercier, Mathieu Nacher, Stéphane Simon, Benoit de Thoisy, Laboratoire de Parasitologie Mycologie [Cayenne, Guyanne Française], Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Ecosystemes Amazoniens et Pathologie Tropicale (EPat), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Guyane (UG), Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP), Neuroépidémiologie Tropicale (NET), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut d'Epidémiologie Neurologique et de Neurologie Tropicale-CHU Limoges-Institut Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST), Université de Limoges (UNILIM)-Université de Limoges (UNILIM), Centre National de Référence (CNR) Toxoplasmose/Toxoplasma Biological Resource Center (BRC) (CNR Toxoplasmose-Toxoplasma BRC), CHU Limoges, Centre d'Investigation Clinique Antilles-Guyane (CIC - Antilles Guyane), CHU de Fort de France-Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française]-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles et de la Guyane (UAG), This work benefited from an 'Investissement d’Avenir' grant managed by the French National Research Agency (ANR) (CEBA, ref. ANR-10-LABX-25-01) and from a European Regional Development Fund (ERDF) grant (FEDER présage n° 30820)., Grelier, Elisabeth, CHU Limoges-Institut d'Epidémiologie Neurologique et de Neurologie Tropicale-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST), and Université des Antilles et de la Guyane (UAG)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -CHU de Fort de France-Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française]
Subjects: Future studies, Genotype, Veterinary (miscellaneous), 030231 tropical medicine, Virulence, Disease, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Mice, 0302 clinical medicine, parasitic diseases, medicine, Animals, Humans, lcsh:RC109-216, Phylogeny, 030304 developmental biology, 0303 health sciences, biology, Obligate, Strain (biology), Amazonian, Toxoplasma gondii, Genetic Variation, biology.organism_classification, medicine.disease, Toxoplasmosis, 3. Good health, Specific Pathogen-Free Organisms, French Guiana, Disease Models, Animal, Infectious Diseases, Toxoplasmosis, Animal, Murine model, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Insect Science, Animal Science and Zoology, Parasitology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Toxoplasma, Microsatellite Repeats, Research Article
Abstract: BACKGROUND: Toxoplasma gondii is an obligate intracellular protozoan parasite of warm-blooded vertebrates. Most infections in immunocompetent patients are asymptomatic. However, since 2000s, strains with particular genetic profiles that differ from the known clonal type (type I, II, III), have been described. In French Guiana, these strains are highly pathogenic in immunocompetent patients. They have defined a new clinical entity called Amazonian Toxoplasmosis. The present study aims to further improve our knowledge on the pathogenicity of these Amazonian T. gondii strains in comparison with three reference strains using Swiss strain mice. With these data, we tried to establish a predictive virulence score to classify these strains, but also to correlate this virulence with the severity of the disease in infected patients.RESULTS: All the virulence indicators revealed that the Amazonian strains isolated in French Guiana presented a high virulence profile, but lower than the highly virulent type I reference RH strain. The findings reveal differences in virulence between human and animal strains, but also between anthropized and wild strains.CONCLUSION: In addition to being a clinically relevant animal model of Amazonian Toxoplasmosis, this model could also provide a solid experimental basis for future studies aiming to investigate the underlying mechanisms of Amazonian Toxoplasmosis disease., Virulence des souches atypiques de Toxoplasma gondii isolées en Guyane française chez un modèle murin. Contexte. Toxoplasma gondii est un parasite protozoaire intracellulaire obligatoire des vertébrés à sang chaud. La plupart des infections chez les patients immunocompétents sont asymptomatiques. Cependant, depuis les années 2000, des souches avec des profils génétiques particuliers qui diffèrent du type clonal connu (type I, II, III) ont été décrites. En Guyane française, ces souches sont hautement pathogènes chez les patients immunocompétents. Elles ont défini une nouvelle entité clinique appelée Toxoplasmose Amazonienne. La présente étude vise à approfondir nos connaissances sur le pouvoir pathogène de ces souches amazoniennes de T. gondii par rapport à 3 souches de référence en utilisant des souris de souche Swiss. Avec ces données, nous avons tenté d'établir un score de virulence prédictif pour classer ces souches mais également de corréler cette virulence avec la gravité de la maladie chez les patients infectés. Résultats. Tous les indicateurs de virulence ont révélé que les souches amazoniennes isolées en Guyane française présentaient une virulence élevée mais plus faible que la souche de référence RH très virulente de type I. Les résultats ont mis en évidence les différences de virulence entre les souches humaines et animales mais aussi entre les souches anthropisées et les souches sauvages. Conclusion. En plus d'être un modèle animal cliniquement pertinent de la toxoplasmose amazonienne, ce modèle pourrait également fournir une base expérimentale solide à de futurs travaux qui chercheront à approfondir les mécanismes sous-jacents de la toxoplasmose amazonienne.
Published: 2019

37. Identification of French Guiana sand flies using MALDI-TOF mass spectrometry with a new mass spectra library

Author: Cécile Nabet, Thiago Vasconcelos dos Santos, Benoit de Thoisy, Anne Cécile Normand, Renaud Piarroux, Marine Ginouves, Magalie Demar, Arthur Kocher, Ghislaine Prévot, Agathe Chavy, Laboratoire des Interactions Virus-Hôtes [Cayenne, Guyane Française], Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Ecosystemes Amazoniens et Pathologie Tropicale (EPat), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Guyane (UG), Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité des Maladies Infectieuses et Tropicales (UMIT), Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Male, RC955-962, Disease Vectors, Forests, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Mass Spectrometry, Analytical Chemistry, 0302 clinical medicine, Spectrum Analysis Techniques, Common species, Arctic medicine. Tropical medicine, Zoonoses, Medicine and Health Sciences, Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry, Phlebotomus / parasitologia, Leishmaniasis, Protozoans, Leishmania, Ecology, Database and informatics methods, Sequence analysis, Leishmaniose / transmiss?o, Eukaryota, Psychodidae / parasitologia, Mass Spectra, Terrestrial Environments, Regi?o Amaz?nica (BR), Vetores de Doen?as, 3. Good health, French Guiana, Chemistry, Infectious Diseases, Physical Sciences, Identification (biology), Female, Public aspects of medicine, RA1-1270, Research Article, Neglected Tropical Diseases, Bioinformatics, 030231 tropical medicine, Zoology, Sequence Databases, Biology, Mass spectrometry, Research and Analysis Methods, Ecosystems, 03 medical and health sciences, Species level, Species Specificity, parasitic diseases, Parasitic Diseases, Animals, DNA sequence analysis, Gene Library, Protozoan Infections, fungi, Ecology and Environmental Sciences, Public Health, Environmental and Occupational Health, Organisms, Biology and Life Sciences, MALDI-TOF Mass Spectrometry, biology.organism_classification, Tropical Diseases, Guiana Francesa (GF), Parasitic Protozoans, Insect Vectors, Sand Flies, Protein profiling, Species Interactions, 030104 developmental biology, Biological Databases, Phlebotomus, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Espectrometria de Massas por Ioniza??o e Dessor??o a Laser Assistida por Matriz / m?todos, Reference database, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie
Abstract: Phlebotomine sand flies are insects that are highly relevant in medicine, particularly as the sole proven vectors of leishmaniasis. Accurate identification of sand fly species is an essential prerequisite for eco-epidemiological studies aiming to better understand the disease. Traditional morphological identification is painstaking and time-consuming, and molecular methods for extensive screening remain expensive. Recent studies have shown that matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a promising tool for rapid and cost-effective identification of arthropod vectors, including sand flies. The aim of this study was to validate the use of MALDI-TOF MS for the identification of Northern Amazonian sand flies. We constituted a MALDI-TOF MS reference database comprising 29 species of sand flies that were field-collected in French Guiana, which are expected to cover many of the more common species of the Northern Amazonian region, including known vectors of leishmaniasis. Carrying out a blind test, all the sand flies tested (n = 157) with a log (score) threshold greater than 1.7 were correctly identified at the species level. We confirmed that MALDI-TOF MS protein profiling is a useful tool for the study of sand flies, including neotropical species, known for their great diversity. An application that includes the spectra generated here will be available to the scientific community in the near future via an online platform., Author summary Phlebotomine sand flies are small insects, mostly known for their role in the transmission of Leishmania parasites to humans and other mammals. In French Guiana, the main clinical form of the disease manifests as cutaneous lesions also called American cutaneous leishmaniasis. The transmission of Leishmania from wild mammals to humans depends on the species of sand fly involved in the transmission. To better understand the mechanism of disease transmission, it is essential to accurately identify sand flies, including both vector and non-vector species. Until now, sand flies have mainly been identified using morphological and molecular methods. Recent studies have shown that a new tool based on protein profiling compiled in a library of spectra may be useful for the identification of arthropod vectors. This tool has the advantage of being less time-consuming, less expensive and does not require technical skills. The aim of this study was to assess the usefulness and accuracy of this new tool in identifying Northern Amazonian sand flies.
Published: 2019

38. A hybrid swarm of manatees along the Guianas coastline, a peculiar environment under the influence of the Amazon River plume

Author: Miriam Marmontel, Anne Lavergne, Fabrício R. Santos, Rafael Félix de Magalhães, Vítor Carvalho, Ana Carolina Oliveira de Meirelles, Benoit de Thoisy, and Camilla S. Lima
Subjects: 0106 biological sciences, 0301 basic medicine, Hybrid zone, Introgression, Amazonian, Population Dynamics, Trichechus manatus, Population, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Rivers, Species Specificity, Guianas coastline, Animals, Trichechus inunguis, Hybrid swarm, lcsh:Science, education, Phylogeny, education.field_of_study, Multidisciplinary, Amazon rainforest, Genetic Variation, Bayes Theorem, Trichechus, Amazon River plume, 030104 developmental biology, Geography, Oceanography, Caribbean Region, Conservation Genetics, Hybridization, Genetic, lcsh:Q, Guyana, Brazil
Abstract: The West Indian (Trichechus manatus) and Amazonian (T. inunguis) manatees have a sympatric occurrence at the mouth of the Amazon River. A result of this interspecific encounter is the occurrence of hybrids, which are frequently found along the coasts of Amapá state in Brazil, French Guiana and Guyana. Here we present new genetic evidence indicating the occurrence of a hybrid swarm along the Guianas Shield coastline, which is an interspecific hybrid zone that also separates T. manatus populations located east (Brazil) and west (Caribbean, Gulf of Mexico, Florida and Antilles). In addition, we suggest that this hybrid population occupies a peculiar mangrove-rich environment under strong influence of the Amazon River plume, which requires an independent management and should be considered a special conservation area.
Published: 2019

39. Ecological niche modelling for predicting the risk of cutaneous leishmaniasis in the Neotropical moist forest biome

Author: Magalie Demar, Jean-François Guégan, Giovanny Herrera, Ghislaine Prévot, Alessandra Nava, Thiago Vasconcelos dos Santos, Benoit de Thoisy, Marine Ginouves, Agathe Chavy, Juan David Ramírez, Sérgio Luiz Bessa Luz, Donnat, Martin, Laboratoires d'excellence - CEnter of the study of Biodiversity in Amazonia - - CEBA2010 - ANR-10-LABX-0025 - LABX - VALID, Laboratoire des Interactions Virus-Hôtes [Cayenne, Guyane Française], Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Ecosystemes Amazoniens et Pathologie Tropicale (EPat), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Guyane (UG), Fundação Oswaldo Cruz (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP), Universidad del Rosario [Bogota], Instituto Evandro Chagas, Laboratoire Hospitalo-Universitaire de Parasitologie-Mycologie, Coordination Régionale de la lutte contre le Virus de L'Immunodéficience Humaine (COREVIH)-Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française]-Université des Antilles (UA), Génétique et évolution des maladies infectieuses (GEMI), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), This study was conducted within the RESERVOIRS program supported by European (ERDF/FEDER) funds and assistance from Collectivité Territoriale de la Guyane and Direction Régionale pour la Recherche et la Technologie, and the MicroBIOME project granted by Laboratoire d'Excellence CEBA 'Investissement d’Avenir' and managed by the Agence Nationale de la Recherche (CEBA, Ref. ANR-10-LABEX-25-01). AC benefits from a PhD grant from the French Guiana University. JFG is sponsored by Institut de Recherche pour le Développement, the Centre National de la Recherche Scientifique, Institut national de la recherche agronomique and Montpellier University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript., ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), Université des Antilles (UA)-Coordination Régionale de la lutte contre le Virus de L'Immunodéficience Humaine (COREVIH)-Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), ANR-10- LABX-25-01,CEBA,Labex CEBA ANR-10- LABX-25-01, de Thoisy, Benoit, and Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ)
Subjects: 0301 basic medicine, Climate, Ecological phenomena and functions, Seasonal variation, RC955-962, Disease transmission, Ecological niche, Biome, Forests, Disease Vectors, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Arctic medicine. Tropical medicine, Zoonoses, Prevalence, Medicine and Health Sciences, Biomass, Leishmaniasis, Mammals, French guiana, Ecology, cutaneous, Altitude, Incidence, Eukaryota, Terrestrial Environments, French Guiana, Santé publique et épidémiologie, Infectious Diseases, Geography, Leishmaniose Cut?nea / transmiss?o, Vertebrates, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Seasons, Public aspects of medicine, RA1-1270, Human, Research Article, Neglected Tropical Diseases, Leishmaniose Cut?nea, Neotropics, Forest Ecology, Ecological Metrics, 030231 tropical medicine, Leishmaniasis, Cutaneous, Skin leishmaniasis, Ecosystems, 03 medical and health sciences, Population Metrics, Cutaneous leishmaniasis, Tropical rain forest, Forest ecology, Parasitic Diseases, medicine, Human footprint, Humans, Animals, [SDV.EE.SANT] Life Sciences [q-bio]/Ecology, environment/Health, Ecosystem, Forest, Environmental temperature, Poverty, Population Density, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, Ecologia / tend?ncias, Protozoan Infections, Population Biology, Ecology and Environmental Sciences, Organisms, Public Health, Environmental and Occupational Health, Biology and Life Sciences, Species Diversity, South America, 15. Life on land, Tropical Diseases, medicine.disease, Human impact on the environment, Ecossistema, Species Interactions, 030104 developmental biology, South america, 13. Climate action, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Anthropology, Vector (epidemiology), Amniotes, Population density, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Season, Species richness, Geographic distribution, Prediction
Abstract: A major challenge of eco-epidemiology is to determine which factors promote the transmission of infectious diseases and to establish risk maps that can be used by public health authorities. The geographic predictions resulting from ecological niche modelling have been widely used for modelling the future dispersion of vectors based on the occurrence records and the potential prevalence of the disease. The establishment of risk maps for disease systems with complex cycles such as cutaneous leishmaniasis (CL) can be very challenging due to the many inference networks between large sets of host and vector species, with considerable heterogeneity in disease patterns in space and time. One novelty in the present study is the use of human CL cases to predict the risk of leishmaniasis occurrence in response to anthropogenic, climatic and environmental factors at two different scales, in the Neotropical moist forest biome (Amazonian basin and surrounding forest ecosystems) and in the surrounding region of French Guiana. With a consistent data set never used before and a conceptual and methodological framework for interpreting data cases, we obtained risk maps with high statistical support. The predominantly identified human CL risk areas are those where the human impact on the environment is significant, associated with less contributory climatic and ecological factors. For both models this study highlights the importance of considering the anthropogenic drivers for disease risk assessment in human, although CL is mainly linked to the sylvatic and peri-urban cycle in Meso and South America., Author summary Cutaneous leishmaniasis is a vector-borne zoonotic disease with a complex transmission cycle that includes many parasite, vector and host species. This disease continues to pose public health problems worldwide despite the measures put in place. In recent years, methodological tools commonly used in ecology, called ecological niche prediction models, have made it possible to determine the environmental and anthropogenic variables that may be favourable to the presence of the host and vector species communities involved in the cycle and therefore to the presence of certain disease agents. The use of these models, based on the presence of human cases of the disease, can overcome some of the uncertainties concerning the diversity of the vectors and the potential hosts involved in the transmission cycle. This approach of health ecology combining ecology and epidemiology could provide new insights into understanding the cycle of disease transmission and the influence of environmental factors and thus improve the prediction of disease emergence and epidemics. It can be applied to various vector-borne diseases whose transmission cycles are still poorly understood and for which studies classically carried out in epidemiology have not prevented disease progression.
Published: 2019

40. Emerging infectious diseases and new pandemics: dancing with a ghost! Lessons in inter- and transdisciplinary research in French Guiana, South America

Author: Jean-François Guégan, Loïc Epelboin, Maylis Douine, Paul Le Turnier, Olivier Duron, Lise Musset, Christine Chevillon, Philippe Quénel, Mark Eric Benbow, and Benoît de Thoisy
Subjects: Biomedical research, Public health, Interdisciplinarity, Transdisciplinarity, One Health, Infectious disease, Infectious and parasitic diseases, RC109-216
Abstract: In light of current international public health challenges, calls for inter- and transdisciplinary research are increasing, particularly in response to complex and intersecting issues. Although widely used under the One Health flag, it is still unclear how inter- and transdisciplinary science should be applied to infectious disease research, public health, and the different stakeholders. Here, we present and discuss our common scientific and biomedical experience in French Guiana, South America to conduct and enrich research in vector-borne and zoonotic infectious diseases, with the aim to translate findings to public health and political stakeholders. We highlight the successful progressive dissolution of disciplinary boundaries that go beyond One Health positive-driven assumptions and argue that specific local conditions, as well as strong support from research and medical institutions, have facilitated an emulsion toward inter- and transdisciplinary science. This argument is intended to improve responses to public health concerns in French Guiana and other countries and regions of the world.
Published: 2023
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41. Q fever epidemic in Cayenne, French Guiana, epidemiologically linked to three-toed sloth

Author: Denis Blanchet, Didier Raoult, Benoit de Thoisy, Jean-Lou Marié, Aba Mahamat, Sophie Edouard, Vincent Pommier de Santi, Carole Ilcinkas, Sébastien Briolant, Georges Hyvert, Bernard Davoust, Yann Reynaud, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Équipe opérationnelle d’hygiène hospitalière, Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Unité des Maladies Infectieuses et Tropicales (UMIT), Direction Interarmées du Service de Santé [Cayenne, Guyane française], Institut Pasteur de la Guadeloupe, Réseau International des Instituts Pasteur (RIIP), Direction Interarmées du Service de Santé en Guyane, Direction Régionale du Service de Santé des Armées (DRSSA - Toulon), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)
Subjects: Adult, Male, 0301 basic medicine, Veterinary medicine, Adolescent, 030231 tropical medicine, 030106 microbiology, Immunology, Attack rate, Three-toed sloth, Animals, Wild, Q fever, Biology, Real-Time Polymerase Chain Reaction, Microbiology, Serology, Young Adult, 03 medical and health sciences, 0302 clinical medicine, Risk Factors, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Zoonoses, medicine, Animals, Humans, Immunology and Allergy, Child, Epidemics, Feces, Disease Reservoirs, Retrospective Studies, General Veterinary, Infant, Outbreak, General Medicine, Middle Aged, biology.organism_classification, Coxiella burnetii, medicine.disease, Sloths, French Guiana, 3. Good health, Infectious Diseases, Child, Preschool, Female, Q Fever, Pneumonia (non-human)
Abstract: International audience; A Q fever epidemic occurred in 2013 in a small military residential area in Cayenne, French Guiana. A retrospective cohort study was conducted to identify Q fever risk factors. Confirmed acute Q fever case was defined as positive serology (IgM >= 50 and phase II IgG >= 200) and/or positive qPCR on serum or blood. In addition, wild mammals were captured at the study site and tested by serology and real-time PCR performed on blood, vaginal swabs and ticks. The attack rate was 20 percent (11/54). All the cases were symptomatic with fever > 38.5 degrees C and community-acquired pneumonia for four cases. Log binomial multivariate models identified two independent risk factors associated with Q fever: to clean the house (RRa = 7.5 CI95% [1.03-55.3]) and to carry a three-toed sloth in arms (RRa = 2.6 CI95% [1.1-5.8]). Eighteen marsupial individuals were captured, all PCRs were negative but 17% (3/18) had a positive serology. Another study conducted after the epidemic found only one (1/4) three-tooth sloth (Bradypus tridactylus) with feces highly infectious for C. burnetii MST17. The same strain C. burnetii genotype 17 has been laboratory-confirmed in this mammal and in human cases. These results support the implication of three-toed-sloth in this epidemic. Human contamination mainly occurs through inhalation of infectious aerosols as suggested by high relative risk associated with house cleaning activities and pulmonary forms of the disease, and through direct contact with three- toed-sloth. Positive serological results among marsupials confirm wildlife exposure and suggest a more complex sylvatic transmission cycle among wild mammals.
Published: 2018

42. Biodiversity in the Amazon: Origin Hypotheses, Intrinsic Capacity of Species Colonization, and Comparative Phylogeography of River Otters (Lontra longicaudis and Pteronura brasiliensis, Mustelidae, Carnivora) and Pink River Dolphin (Inia sp., Iniidae, Cetacea)

Author: Josep Mark Shostell, Myreya Pinedo-Castro, Manuel Ruiz-García, Pablo Escobar-Armel, María Martínez-Agüero, and Benoit de Thoisy
Subjects: 0106 biological sciences, 0301 basic medicine, Mustelidae, Biodiversity, Amazon biodiversity, Pteronura, 010603 evolutionary biology, 01 natural sciences, Mitochondrial markers, Otter, Iniidae, 03 medical and health sciences, Inia, biology.animal, Systematics, Lontra, Ecology, Evolution, Behavior and Systematics, Phylogeny, biology, Ecology, River dolphin, biology.organism_classification, Phylogeography, 030104 developmental biology
Abstract: We sequenced mitochondrial genes of otter (Lontra longicaudis and Pteronura brasiliensis) and dolphin (Inia sp.) species to provide new systematics data and to test hypotheses that offer explanations as to the Amazon’s biodiversity. Four of the 11 hypotheses tested --Paleogeography (PH), Recent Lagoon (RLH), Hydrogeological Recent Change (HRCH), and Refugia (RH)-- support the evolution of these three species. As part of this comparative phylogenetic study, we also considered the degree of water dependence of each species. For the least water dependent of the three species, L. longicaudis, only HRCH and RH had an influence on genetic structure, although it was relatively minor. For the more water dependent otter species, P. brasiliensis, our analyses stressed the significance of a single PH event along with two lesser important PH events. However, its gene diversification basically occurred during the Pleistocene and our analyses did detect a relatively small influence of HRCH and RH. For the completely water dependent species, Inia, we detected two significant PH events. Its genetic structure was considerably more developed than in either otter species, although the Pleistocene was a very important period of genetic diversification for the pink river dolphins (HRCH and RLH). Each species has ancestors with different geographical origins and genomes with different capacities to colonize—making it difficult to rely on a generalized hypothesis to understand the origins of the Amazon’s extremely rich biodiversity. © 2017, Springer Science+Business Media New York.
Published: 2018

43. The role of Pleistocene climate change in the genetic variability, distribution and demography of Proechimys cuvieri and P. Guyannensis (Rodentia: Echimyidae) in northeastern Amazonia

Author: François Catzeflis, Claudia Regina Silva, Camila C. Ribas, Maria Nazareth Ferreira da Silva, Rafael N. Leite, Duke S. Rogers, Benoit de Thoisy, Instituto Nacional de Pesquisas da Amazônia (INPA), Instituto de Pesquisas Científicas e Tecnológicas do Estado do Amapá (IEPA), Estado do Amapa, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Brigham Young University (BYU), Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP), We thank Fundação de Amparo à Pesquisa do Estado do Amapá (FAPEAP), Fundação de Amparo à Pesquisa do Estado do Amazonas (FAPEAM) and Intitut de Recherche pour le Développement (IRD) for financial support through the Guyamazon II research program (Process 250203021/2014). The project benefited from the support of an ‘‘Investissement d’Avenir’’ grant managed by Agence Nationale de la Recherche (CEBA, Ref. ANR-10-LABX-25-01). We also thank FAPEAP for support through the Thesis Funding Programme (Process 250203052/2014). CRS thanks Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) for a scholarship. RNL was supported by CNPq (150069 / 2014-6, 457267 / 2014-3)., Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Sympatry, Proechimys Guyannensis, Heredity, Genetic Distance, Marine and Aquatic Sciences, Forests, 01 natural sciences, Geographical locations, Species Habitat, Pleistocene Epoch, Haplotype, Proechimys cuvieri, Phylogeny, Data Management, River, Animalss, Quaternary Period, Multidisciplinary, Rodent, Geography, Ecology, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Species Distribution, Geology, Phylogenetic Analysis, Cytochromes b, Terrestrial Environments, Phylogenetics, Pleistocene, Genetic Mapping, Phylogeography, Biogeography, Genetic Variability, Genetic structure, Medicine, Proechimys guyannensis, Gene Structures, Brazil, Research Article, Freshwater Environments, Systematics, Computer and Information Sciences, Gene Sequence, Science, Climate Change, Rodentia, Cytochromes B, 010603 evolutionary biology, Ecosystems, Proechimys Cuvieri, 03 medical and health sciences, Rivers, Animals Tissue, Genetics, Molecular Clock, Animals, Evolutionary Systematics, Controlled Study, Taxonomy, Demography, Evolutionary Biology, Population Biology, Brasil, Ecology and Environmental Sciences, Cytochrome B, Biology and Life Sciences, Aquatic Environments, Paleontology, Genetic Variation, Geologic Time, Bayes Theorem, Echimyidae, Bodies of Water, South America, 15. Life on land, biology.organism_classification, Nonhuman, 030104 developmental biology, Haplotypes, Earth Sciences, Cenozoic Era, Species richness, People and places, Paleogenetics, Population Genetics
Abstract: The spiny rats, genus Proechimys, have the highest species richness within the Echimyidae family, as well as species with high genetic variability. The genus distribution includes tropical South America and Central America south to Honduras. In this study, we evaluate the phylogeographic histories of Proechimys guyannensis and P. cuvieri using cytochrome b, in a densely sampled area in northeastern Amazon where both species are found in sympatry in different environments. For each species, Bayesian and Maximum Likelihood phylogenetic analysis were congruent and recovered similar clades in the studied area. Bayesian phylogenetic analysis using a relaxed molecular clock showed that these clusters of haplotypes diversified during Pleistocene for both species. Apparently, the large rivers of the region did not act as barriers, as some clades include specimens collected from opposite banks of Oiapoque, Araguari and Jari rivers. Bayesian skyline plot analysis showed recent demographic expansion in both species. The Pleistocene climatic changes in concert with the geologic changes in the Amazon fan probably acted as drivers in the diversification that we detected in these two spiny rats. Proechimys cuvieri and P. guyannensis show genetic structure in the eastern part of the Guiana region. Greater genetic distances observed in P. guyannensis, associated with highly structured groups, suggest that more detailed studies of systematics and ecology should be directed to this species. © 2018 Silva et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Published: 2018

44. Green turtle (Chelonia mydas) genetic diversity at Paranaguá Estuarine Complex feeding grounds in Brazil

Author: Flavia Maria Guebert, Juliana Costa Jordao, Ana Cristina Vigliar Bondioli, Lurdes Foresti de Almeida Toledo, and Benoit de Thoisy
Subjects: geography, Genetic diversity, education.field_of_study, geography.geographical_feature_category, Chelonia mydas, lcsh:QH426-470, Demographic history, Ecology, mtDNA, Foraging, Population, Last Glacial Maximum, Estuary, mixed stock analysis, Biology, lcsh:Genetics, connectivity, Genetics, Juvenile, education, Protected area, Animal Genetics, Molecular Biology, feeding grounds
Abstract: Sea turtles are marine reptiles that undertake long migrations through their life, with limited information regarding juvenile stages. Feeding grounds (FGs), where they spend most of their lives, are composed by individuals from different natal origins, known as mixed stock populations. The aim of this study was to assess genetic composition, natal origins and demographic history of juvenile green turtles (Chelonia mydas) at the Paranaguá Estuarine Complex (PEC), Brazil, considered a Natural World Heritage site. Tissue samples of stranded animals were collected (n = 60), and 700 bp mitochondrial DNA sequences were generated and compared to shorter sequences from previously published studies. Global exact tests of differentiation revealed significant differences among PEC and the other FGs, except those at the South Atlantic Ocean. Green turtles at PEC present genetic signatures similar to those of nesting females from Ascension Island, Guinea Bissau and Aves Island/Surinam. Population expansion was evidenced to have occurred 20-25 kYA, reinforcing the hypothesis of recovery from Southern Atlantic refugia after the last Glacial Maximum. These results contribute to a better understanding of the dynamics of green turtle populations at a protected area by providing knowledge on the dispersion patterns and reinforcing the importance of the interconnectivity between nesting and foraging populations.
Published: 2015

45. iDNA screening: Disease vectors as vertebrate samplers

Author: Anne-Laure Bañuls, Jérôme Murienne, François Catzeflis, Arthur Kocher, Benoit de Thoisy, Sophie Valière, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP), Laboratoire de Paléontologie-Paléobiologie-Phylogénie (UMR CNRS 5554), Université Montpellier 2 - Sciences et Techniques (UM2), Département de Génétique Animale [Toulouse], Institut National de la Recherche Agronomique (INRA), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Agence Nationale de la Recherche. Grant Numbers: ANR‐10‐LABX‐25‐01, ANR‐10‐LABX‐41, ANR‐11‐IDEX‐0002‐02, LABEX DRIIHM ANR-11-LABX-0010, ANR-11-LABX-0010/11-LABX-0010,LabEx DRIIHM,Dispositif de recherche interdisciplinaire sur les Interactions Hommes-Milieux(2011), ANR-10- LABX-25-01,CEBA,Labex CEBA ANR-10- LABX-25-01, ANR-11-IDEX-0002-02/10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2011), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Du gène à l'écosystème (MIVEGEC-GeneSys), Pathogènes, Environnement, Santé Humaine (EPATH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), ANR-11-LABX-0010,DRIIHM / IRDHEI,Dispositif de recherche interdisciplinaire sur les Interactions Hommes-Milieux(2011), ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), and ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011)
Subjects: 0106 biological sciences, 0301 basic medicine, Arboreal locomotion, bloodmeal, media_common.quotation_subject, Fauna, [SDV]Life Sciences [q-bio], Biodiversity, mosquito, Insect, Biology, 010603 evolutionary biology, 01 natural sciences, Field methods, 03 medical and health sciences, biology.animal, parasitic diseases, Genetics, Animals, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, media_common, Invertebrate, Ecology, Vertebrate, dipteran, DNA, Feeding Behavior, 15. Life on land, biology.organism_classification, French Guiana, Insect Vectors, feeding preference, Culicidae, 030104 developmental biology, Evolutionary biology, Vertebrates, insect, Arthropod, sand fly, Psychodidae
Abstract: International audience; In the current context of global change and human-induced biodiversity decline, there is an urgent need for developing sampling approaches able to accurately describe the state of biodiversity. Traditional surveys of vertebrate fauna involve time-consuming and skill-demanding field methods. Recently, the use of DNA derived from invertebrate parasites (leeches and blowflies) was suggested as a new tool for vertebrate diversity assessment. Bloodmeal analyses of arthropod disease vectors have long been performed to describe their feeding behaviour, for epidemiological purposes. On the other hand, this existing expertise has not yet been applied to investigate vertebrate fauna per se. Here, we evaluate the usefulness of hematophagous dipterans as vertebrate samplers. Blood-fed sand flies and mosquitoes were collected in Amazonian forest sites and analysed using high-throughput sequencing of short mitochondrial markers. Bloodmeal identifications highlighted contrasting ecological features and feeding behaviour among dipteran species, which allowed unveiling arboreal and terrestrial mammals of various body size, as well as birds, lizards and amphibians. Additionally, lower vertebrate diversity was found in sites undergoing higher levels of human-induced perturbation. These results suggest that, in addition to providing precious information on disease vector host use, dipteran bloodmeal analyses may represent a useful tool in the study of vertebrate communities. Although further effort is required to validate the approach and consider its application to large-scale studies, this first work opens up promising perspectives for biodiversity monitoring and eco-epidemiology.
Published: 2017

46. Evaluation of short mitochondrial metabarcodes for the identification of Amazonian mammals

Author: Mailis Huguin, Arthur Kocher, Jérôme Murienne, Lucie Zinger, Sophie Valière, François Catzeflis, Anne-Laure Bañuls, Benoit de Thoisy, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Association Kwata (Kwata), Kwata, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Département de Génétique Animale [Toulouse], Institut National de la Recherche Agronomique (INRA), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Du gène à l'écosystème (MIVEGEC-GeneSys), Pathogènes, Environnement, Santé Humaine (EPATH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Investissement d'Avenir CEBA: ANR-10-LABX-25-01 TULIP: ANR-10-LABX-41 ANR-11-IDEX-0002-02 / project METABAR ANR-11-BSV7-0020, Université de Toulouse (UT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Amazonian, blood meals, Biology, MT-RNR1, Barcode, DNA barcoding, law.invention, COI, 03 medical and health sciences, law, parasitic diseases, mitochondrial 12S rRNA gene, Ecology, Evolution, Behavior and Systematics, Ecology, Ecological Modeling, Ribosomal RNA, French Guiana, 030104 developmental biology, Evolutionary biology, Reference database, Identification (biology), Primer (molecular biology), sand fly, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; 1. DNA barcoding and metabarcoding are increasingly used as alternatives to traditional morphological identifications. For animals, the standard barcode is a c. 658-bp portion of the COI gene, for which reference libraries now cover a large proportion of described mammal species. Unfortunately, because its sequence is too long and does not contain highly conserved primer binding sites, this marker is not adapted for metabarcoding. Although alternative metabarcodes have been developed, their performances are generally seldom assessed. 2. We evaluate the reliability of a short metabarcode located in the mitochondrial 12S ribosomal RNA for the identifications of Amazonian mammals. We (i) constitute a nearly exhaustive reference library for species found in French Guiana, (ii) assess the taxonomic resolution of the marker and validate its use with dipteran blood meal analyses, (iii) assess the conservation of the primer binding sites, and (iv) compare its theoretical performances with that of a newly designed metabarcode located within the standard COI barcode. 3. About 576 specimens representing 164 species were gathered and sequenced. We show that the 12S marker allows remarkably accurate taxonomic assignations despite its very short size, and that primer binding sites are highly conserved, which is important to avoid PCR amplification bias potentially leading to detection failure. Additionally, our results stress that the identifications should only be considered at the generic level when they are based on incomplete reference libraries, even when a stringent similarity cutoff is used. A new short COI metabarcode was designed based on 569 reference sequences of mammals retrieved on BOLD. Our results clearly show that, while both markers provide similar taxonomic resolution, much higher rates of primer mismatches are found with COI. 4. Besides demonstrating the accuracy of the short 12S marker for the identification of Amazonian mammals and providing a reliable molecular reference database, this study emphasizes that the accuracy of taxonomic assignations highly depends on the comprehensiveness of the reference library and that great caution should be taken for interpreting metabarcoding results based on scarce reference libraries. The comparison with a short COI metabarcode also provides novel evidence in support for the use of ribosomal markers in metabarcoding studies.
Published: 2017

47. The Gulf Stream frontal system: A key oceanographic feature in the habitat selection of the leatherback turtle?

Author: Simon Benhamou, Mathieu Brucker, Fabien Roquet, Philippine Chambault, Alberto Baudena, Etienne Pauthenet, Benoit de Thoisy, Rodrigue Crasson, Marc Bonola, Yvon Le Maho, Virginie Dos Reis, Damien Chevallier, Département Ecologie, Physiologie et Ethologie (DEPE-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Department of Meteorology, Stockholm University, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Association Kwata, Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), and Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: 0106 biological sciences, Satellite tracking, Mixed layer, Halocline, Aquatic Science, Oceanography, 010603 evolutionary biology, 01 natural sciences, Dermochelys coriacea, Water column, Ocean gyre, 14. Life underwater, geography.geographical_feature_category, 010604 marine biology & hydrobiology, Post-nesting migration, North Atlantic, Sea-surface height, Diving behaviour, Gulf Stream, Sea surface temperature, Geography, 13. Climate action, Climatology, [SDE]Environmental Sciences, Thermocline
Abstract: Although some associations between the leatherback turtle Dermochelys coriacea and the Gulf Stream current have been previously suggested, no study has to date demonstrated strong affinities between leatherback movements and this particular frontal system using thorough oceanographic data in both the horizontal and vertical dimensions. The importance of the Gulf Stream frontal system in the selection of high residence time (HRT) areas by the North Atlantic leatherback turtle is assessed here for the first time using state-of-the-art ocean reanalysis products. Ten adult females from the Eastern French Guianese rookery were satellite tracked during post-nesting migration to relate (1) their horizontal movements to physical gradients (Sea Surface Temperature (SST), Sea Surface Height (SSH) and filaments) and biological variables (micronekton and chlorophyll a ), and (2) their diving behaviour to vertical structures within the water column (mixed layer, thermocline, halocline and nutricline). All the turtles migrated northward towards the Gulf Stream north wall. Although their HRT areas were geographically remote (spread between 80–30 °W and 28–45 °N), all the turtles targeted similar habitats in terms of physical structures, i.e. strong gradients of SST, SSH and a deep mixed layer. This close association with the Gulf Stream frontal system highlights the first substantial synchronization ever observed in this species, as the HRTs were observed in close match with the autumn phytoplankton bloom. Turtles remained within the enriched mixed layer at depths of 38.5±7.9 m when diving in HRT areas, likely to have an easier access to their prey and maximize therefore the energy gain. These depths were shallow in comparison to those attained within the thermocline (82.4±5.6 m) while crossing the nutrient-poor subtropical gyre, probably to reach cooler temperatures and save energy during the transit. In a context of climate change, anticipating the evolution of such frontal structure under the influence of global warming is crucial to ensure the conservation of this vulnerable species.
Published: 2017

48. Habitat use and diving behaviour of gravid olive ridley sea turtles under riverine conditions in French Guiana

Author: Yvon Le Maho, Laurent Kelle, Marc Bonola, Damien Chevallier, Lucie Giraudou, Benoit de Thoisy, Philippine Chambault, Virginie Dos Reis, Fabian Blanchard, Département Ecologie, Physiologie et Ethologie (DEPE-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Association Kwata (Kwata), Kwata, WWF Guyane, Laboratoire Ecologie, Evolution, Interactions des Systèmes amazoniens (LEEISA), Centre National de la Recherche Scientifique (CNRS)-Université de Guyane (UG)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), CARET2 program (n°211/04/05), and Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Range (biology), Foraging, Lepidochelys olivacea, Aquatic Science, Oceanography, Generalist and specialist species, 010603 evolutionary biology, 01 natural sciences, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, Inter-nesting season, Rookery, Equatorial Atlantic, biology, Ecology, Amazon rainforest, 010604 marine biology & hydrobiology, Amazon River, biology.organism_classification, Behavioural synchrony, Fishery, Sea turtle, Geography, Habitat, [SDE]Environmental Sciences
Abstract: The identification of the inter-nesting habitat used by gravid sea turtles has become a crucial factor in their protection. Their aggregation in large groups of individuals during the inter-nesting period exposes them to increased threats to their survival - particularly along the French Guiana shield, where intense legal and illegal fisheries occur. Among the three sea turtle species nesting in French Guiana, the olive ridley appears to have the most generalist diet, showing strong behavioural plasticity according to the environment encountered. The large amounts of sediments that are continuously discharged by the Amazon River create a very unusual habitat for olive ridleys, i.e. turbid waters with low salinity. This study assesses the behavioural adjustments of 20 adult female olive ridleys under such riverine conditions. Individuals were tracked by satellite from Remire-Montjoly rookery in French Guiana using tags that recorded the location and diving parameters of individuals, as well as the immediate environment of the turtles including the in situ temperature and salinity. Data concerning potential preys was provided via collection of epifauna by a trawler. Multiple behavioural shifts were observed in both horizontal and vertical dimensions. During the first half of the inter-nesting season, the turtles moved away from the nesting beach (21.9 ± 24.7 km ), performing deeper (12.6 ± 7.4 m) and longer (29.7 ± 21.0 min) dives than during the second half of the period (7.4 ± 7.8 km, 10.4 ± 4.9 m and 25.9 ± 19.3 min). Olive ridleys remained in waters that were warm (range: 26–33 °C) and which fluctuated in terms of salinity (range: 19.5–36.4 psu), in a relatively small estuarine habitat covering 423 km 2 . If olive ridleys were foraging during this period, the potential preys that might be available were mostly crustaceans (43%) and fish (39%), as expected for the diet of this generalist species during this period. This study highlights the numerous behavioural adaptations of this species in response to the unusual riverine conditions of the French Guiana continental shelf.
Published: 2017

49. Distribution of the habitat suitability of the main malaria vector in French Guiana using maximum entropy modeling

Author: Emmanuel Roux, Romain Girod, Isabelle Dusfour, Sébastien Briolant, Benoit de Thoisy, Yi Moua, Frédérique Seyler, Université de Guyane (UG), UMR 228 Espace-Dev, Espace pour le développement, Université de Guyane (UG)-Université des Antilles (UA)-Institut de Recherche pour le Développement (IRD)-Université de Perpignan Via Domitia (UPVD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM), Institut de Recherche pour le Développement (IRD), Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP), Direction Interarmées du Service de Santé en Guyane, Institut de Recherche Biomédicale des Armées (IRBA), Institut de Recherche pour le Développement (IRD)-Université de Perpignan Via Domitia (UPVD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM)-Université de Guyane (UG)-Université des Antilles (UA), and Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)
Subjects: 0106 biological sciences, Amazonian, 030231 tropical medicine, Species distribution, Geographic Mapping, Biology, Spatial distribution, 010603 evolutionary biology, 01 natural sciences, Models, Biological, 03 medical and health sciences, 0302 clinical medicine, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Anopheles, parasitic diseases, Animals, Anopheles darlingi, Ecosystem, Sampling bias, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, [STAT.AP]Statistics [stat]/Applications [stat.AP], presence-only, General Veterinary, Ecology, species distribution model, Principle of maximum entropy, 15. Life on land, biology.organism_classification, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, sampling bias, French Guiana, Insect Vectors, Malaria, Infectious Diseases, Habitat, Insect Science, Vector (epidemiology), Parasitology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Maxent, Cartography, Animal Distribution, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: International audience; Malaria is an important health issue in French Guiana. Its principal mosquito vector in this region is Anopheles darlingi Root. Knowledge of the spatial distribution of this species is still very incomplete due to the extent of French Guiana and the difficulty to access most of the territory. Species distribution modeling based on the maximal entropy procedure was used to predict the spatial distribution of An. darlingi using 39 presence sites. The resulting model provided significantly high prediction performances (mean 10-fold cross-validated partial area under the curve and continuous Boyce index equal to, respectively, 1.11—with a level of omission error of 20%—and 0.42). The model also provided a habitat suitability map and environmental response curves in accordance with the known entomological situation. Several environmental characteristics that had a positive correlation with the presence of An. darlingi were highlighted: non-permanent anthropogenic changes of the natural environment, the presence of roads and tracks, and opening of the forest. Some geomorphological landforms and high altitude landscapes appear to be unsuitable for An. darlingi. The species distribution modeling was able to reliably predict the distribution of suitable habitats for An. darlingi in French Guiana. Results allowed completion of the knowledge of the spatial distribution of the principal malaria vector in this Amazonian region, and identification of the main factors that favor its presence. They should contribute to the definition of a necessary targeted vector control strategy in a malaria pre-elimination stage, and allow extrapolation of the acquired knowledge to other Amazonian or malaria-endemic contexts.
Published: 2017

50. Mixed-stock analysis in green turtles Chelonia mydas: mtDNA decipher current connections among west Atlantic populations

Author: Rachel Berzins, Yvon Le Maho, Damien Chevallier, Juliana Costa Jordao, Ana Cristina Vigliar Bondioli, Benoit de Thoisy, Karin Bilo, Lurdes Foresti de Almeida-Toledo, Instituto de Biociências, Universidade de São Paulo (USP), Instituto de Biociências, Universidade de São Paulo, Instituto de Pesca-APTA-SAA/SP, WWF Suriname, Office National de la Chasse et de la Faune Sauvage [Kourou, Guyane], Université des Antilles (Pôle Guadeloupe), Université des Antilles (UA)-Université des Antilles (UA)-Institut National de la Recherche Agronomique (INRA)-Université de Guyane (UG)-Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Centre National de la Recherche Scientifique (CNRS)-AgroParisTech, Département Ecologie, Physiologie et Ethologie (DEPE-IPHC), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Association Kwata (Kwata), Kwata, Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (Pôle Guadeloupe), Université des Antilles (UA)-Université des Antilles (UA), Institut Pluridisciplinaire Hubert Curien (IPHC), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (Pôle Guadeloupe), and Institut National de la Recherche Agronomique (INRA)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université des Antilles (Pôle Guadeloupe)
Subjects: Gene Flow, 0106 biological sciences, Mitochondrial DNA, Population structure, nesting areas, gene flows, Biology, Chelonia, DNA, Mitochondrial, 010603 evolutionary biology, 01 natural sciences, feeding areas, MSA, Genetics, Animals, 14. Life underwater, Atlantic Ocean, Molecular Biology, Stock (geology), mtDNA control region, Ecology, 010604 marine biology & hydrobiology, Genetic Variation, Sequence Analysis, DNA, control region, Turtles, Phylogeography, Genetics, Population, Haplotypes, Guinea bissau, Genome, Mitochondrial, [SDE]Environmental Sciences, Female, Brazil, Genetic composition
Abstract: International audience; The green turtle Chelonia mydas undertakes wide-ranging migrations between feeding and nestingsites, resulting in mixing and isolation of genetic stocks. We used mtDNA control region tocharacterize the genetic composition, population structure, and natal origins of C. mydas in theWest Atlantic Ocean, at one feeding ground (State of Rio de Janeiro, Brazil), and three Caribbeannesting grounds (French Guiana, Guadeloupe, and Suriname). The feeding ground presentedconsiderable frequency of common haplotypes from the South Atlantic, whereas the nesting sitespresented a major contribution of the most common haplotype from the Caribbean. MSA revealedmultiple origins of individuals at the feeding ground, notably from Ascension Island, Guinea Bissau,and French Guiana. This study enables a better understanding of the dispersion patterns andhighlights the importance of connecting both nesting and feeding areas. Effective conservationinitiatives need to encompass these ecologically and geographically distinct sites as well as thosecorridors connecting them.
Published: 2017

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