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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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28. 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

29. Comparative transcriptomics reveals divergent paths of chitinase evolution underlying dietary convergence in ant-eating mammals

Author

Rémi Allio, Sophie Teullet, Dave Lutgen, Amandine Magdeleine, Rachid Koual, Marie-Ka Tilak, Benoit de Thoisy, Christopher A. Emerling, Tristan Lefébure, and Frédéric Delsuc

Abstract

Ant-eating mammals represent a textbook example of convergent evolution. Among them, anteaters and pangolins exhibit the most extreme convergent phenotypes with complete tooth loss, elongated skulls, protruding tongues, hypertrophied salivary glands producing large amounts of saliva, and powerful claws for ripping open ant and termite nests. However, comparative genomic analyses have shown that anteaters and pangolins differ in their chitinase gene (CHIA) repertoires, which potentially degrade the chitinous exoskeletons of ingested ants and termites. While the southern tamandua (Tamandua tetradactyla) harbors four functionalCHIAparalogs (CHIA1-4), Asian pangolins (Manisspp.) have only one functional paralog (CHIA5). Here, we performed a comparative transcriptomic analysis of salivary glands in 33 placental species, including 16 novel transcriptomes from ant-eating species and close relatives. Our results suggest that salivary glands play an important role in adaptation to an insect-based diet, as expression of differentCHIAparalogs is observed in insectivorous species. Furthermore, convergently-evolved pangolins and anteaters express different chitinases in their digestive tracts. In the Malayan pangolin,CHIA5is overexpressed in all major digestive organs, whereas in the southern tamandua, all four functional paralogs are expressed, at very high levels forCHIA1andCHIA2in the pancreas, and forCHIA3andCHIA4in the salivary glands, stomach, liver, and pancreas. Overall, our results demonstrate that divergent molecular mechanisms underlie convergent adaptation to the ant-eating diet in pangolins and anteaters. This study highlights the role of historical contingency and molecular tinkering of the chitin-digestive enzyme toolkit in this classic example of convergent evolution.

Published
2022

30. Evidence of backcross inviability and mitochondrial DNA paternal leakage in sea turtle hybrids

Author

Sibelle T. Vilaça, Francesco Maroso, Paulo Lara, Benoit de Thoisy, Damien Chevallier, Larissa Souza Arantes, Fabricio R. Santos, Giorgio Bertorelle, and Camila J. Mazzoni

Subjects
Marine turtles, ddRAD, Genetics, RADseq, hybridization, DNA, Mitochondrial/genetics [MeSH], Polymerase Chain Reaction [MeSH], Turtles/genetics [MeSH], Animals [MeSH], Mitochondria/genetics [MeSH], introgression, marine turtles, mitogenomes, Biological Evolution [MeSH], Ecology, Evolution, Behavior and Systematics, hybrid breakdown
Abstract

This dataset contains ddRAD data used in our sea turtles genomics research on hybridization in Brazil. In this paper, we analyzed hybridization patterns, population structure and relatedness between southwest Atlantic population with a focus on Brazilian populations with high frequency of interspecific hybrids. Source code for the R2SCO pipeline is available at https://github.com/mazzoni-izw/mazzoni-begendiv/ and raw sequencing data is available on on NCBI Sequence Read Archive (SRA) database under BioProject PRJNA857276. Data uploaded here contain: Hybrids_SNPs.vcf: SNP dataset for population analyses. Hybrids_SNPs_DP15.recode.vcf: SNP dataset for population analyses filtered for a minimum coverage (DP) of 15 R2SCO-MseI-EcoRI-384-448_CcEiHyb.fasta: reference fasta sequences (R2SCO loci) used to map raw reads from loggerheads, hawksbills and their hybrids. Generated using the R2SCO pipeline described in Driller et al (2020) R2SCO-MseI-EcoRI-384-448_CcEiLoCm.fasta: reference fasta sequences (R2SCO loci) used to map raw reads from loggerheads, hawksbills, olive ridleys, green turtles, and their hybrids. Generated using the R2SCO pipeline described in Driller et al (2020) checkRestrictionSites.py: custom script that filters a fastq file to start and end with defined sequences Structure folder Create_Haplotype_Structure.py: python script used to convert the VCF output from Stacks populations into a Structure file based on haplotypes (instead of SNPs). Hybrids_Haps_DP15.str: input structure file for haplotypes dataset Hybrids_SNPs_DP15.stru input structure file for SNP dataset ParallelStructure_HAPS.R: Command line used in parallel structure for haplotype dataset ParallelStructure_SNPs.R: Command line used in parallel structure for SNP dataset relatedness folder populations.snps.vcf.gz: VCF file of SNP dataset with only loggerheads, hawksbills and their hybrids run.sh: vcftools command line used to run relatedness analysis relatednessmatrix.relatedness: square matrix with relatedness estimates inds.txt: individuals included in the square matrix. relatedness.R: plotting script in R for relatedness results (figure 3) NewHybrids folder Hybrids.NewHyb.input: input file for NewHybrids analysis., Hybridization is known to be part of many species' evolutionary history. Sea turtles have a fascinating hybridization system in which species separated by as much as 43 million years are still capable of hybridizing. Indeed, the largest nesting populations in Brazil of loggerheads (Caretta caretta) and hawksbills (Eretmochelys imbricata) have a high incidence of hybrids between these two species. A third species, olive ridleys (Lepidochelys olivacea), is also known to hybridize although at a smaller scale. Here we used restriction site-associated DNA sequencing (RAD-Seq) markers, mitogenomes, and satellite-telemetry to investigate the patterns of hybridization and introgression in the Brazilian sea turtle population and their relationship with the migratory behaviors between feeding and nesting aggregations. We also explicitly test if the mixing of two divergent genomes in sea turtle hybrids causes mitochondrial paternal leakage. We developed a new species-specific PCR-assay capable of detecting mitochondrial DNA (mtDNA) inheritance from both parental species and performed ultra-deep sequencing to estimate the abundance of each mtDNA type. Our results show that all adult hybrids are first generation (F1) and most display a loggerhead migratory behavior. We detected paternal leakage in F1 hybrids and different proportions of mitochondria from maternal and paternal species. Although previous studies showed no significant fitness decrease in hatchlings, our results support genetically-related hybrid breakdown possibly caused by cytonuclear incompatibility. Further research on hybrids from other populations besides Brazil and between different species will show if backcross inviability and mitochondrial paternal leakage is observed across sea turtle species., {"references":["Driller et al. (2020). BioRXiv. doi: https://doi.org/10.1101/2020.04.03.024331"]}

Published
2022

31. Leprosy Transmission in Amazonian Countries: Current Status and Future Trends

Author

Rodolphe E. Gozlan, Carolina Talhari, Ramanuj Lahiri, Roxane Schaub, Pierre Couppié, Lucibel Crespo, Richard W. Truman, Benoit de Thoisy, John Jairo Dávila, Maria Paredes Larrea, Pedro Legua, Josafá Gonçalves Barreto, Purna Dwivedi, Nora Cardona-Castro, Charlotte Avanzi, Heather Morris-Wilson, Alberto Paniz-Mondolfi, Pushpendra Singh, and Karin Sewpersad

Subjects
0301 basic medicine, Armadillos, medicine.medical_specialty, Ecology (disciplines), Amazonian, 030231 tropical medicine, 030106 microbiology, Disease, 03 medical and health sciences, 0302 clinical medicine, Amazonia, Leprosy, medicine, Immunology and Allergy, Guianas, Socioeconomics, Transmission (medicine), Public health, Zoonosis, South America, medicine.disease, 3. Good health, Mycobacterium leprae, Infectious Diseases, One Health, Geography, purl.org/pe-repo/ocde/ford#3.03.06 [https]
Abstract

Purpose of ReviewLeprosy is one of the first pathologies described in the history of mankind. However, the ecology, transmission, and pathogenicity of the incriminated bacilli remain poorly understood. Despite effective treatment freely distributed worldwide since 1995, around 200,000 new cases continue to be detected yearly, mostly in the tropics. This review aims to discuss the unique characteristics of leprosy in Amazonian countries, which exhibit a very heterogeneous prevalence among human and animal reservoirs.Recent FindingsGroundbreaking discoveries made in the last 15 years have challenged the dogmas about leprosy reservoirs, transmission, and treatment. The discovery of a new leprosy causative agent in 2008 and the scientific proof of zoonosis transmission of leprosy by nine-banded armadillos in the southern USA in 2011 challenged the prospects of leprosy eradication. In the Amazonian biome, nine-banded and other armadillo species are present but the lack of large-scale studies does not yet allow accurate assessment of the zoonotic risk. Brazil is the second country in the world reporting the highest number of new leprosy cases annually. The disease is also present, albeit with different rates, in all neighboring countries. Throughout the Amazonian biome, leprosy is mainly found in hyperendemic foci, conducive to the emergence and transmission of drug-resistant strains.SummaryThe deepening of current knowledge on leprosy reservoirs, transmission, and therapeutic issues, with the One Health approach and the help of molecular biology, will allow a better understanding and management of the public health issues and challenges related to leprosy in Amazonia.

Published
2020

32. Study and conservation of the Guiana Dolphin (Sotalia guianensis) (Van Bénéden, 1864) in French Guiana

Author

Amandine Bordin, Margot Vanhoucke, Kévin Pineau, Laurent Kelle, Nolwenn Cozannet, Monique Pool, Jaime Bolaños-Jiménez, and Benoit De Thoisy

Abstract

The Guiana dolphin (Sotalia guianensis) occurs in warm and shallow waters of the Atlantic Ocean and the Caribbean Sea, from southern Brazil to Honduras, including estuarine and freshwater habitats such as Maracaibo Lake (Venezuela), and the Orinoco River. In 2018, the Guiana dolphin was reclassified from Data Deficient to Near Threatened on the global IUCN Red List. Nevertheless, the conservation status identified by national and regional Red Lists is even more alarming. In French Guiana, for example, the species is classified as Endangered based on strong pressures such as bycatch. In this region, the Guiana dolphin inhabits river mouths and coastal waters where most anthropogenic activities occur. Better knowledge of the biology and ecology is needed in French Guiana to help inform effective conservation actions. Here, we present ongoing studies to map the distribution of Guiana dolphins along the French Guiana coast and estimate abundance in a hotspot area. Aerial survey campaigns were conducted during the dry season in 2013, 2014, 2015, and 2019. Eight flights were conducted and 146 dolphins belonging to 39 groups were observed. Boat-based line-transect surveys were also conducted in the coastal waters of Cayenne in 2017 and 2018. Twenty-one survey trips were conducted covering 999.06 km. Three hundred and eighty-two dolphins belonging to 63 groups were observed. The total abundance in the Cayenne area was estimated at 128 dolphins (% CV = 30.92; CI (95%) = 70-235) with a density of 0.80 ind./km² (% CV = 30.92; CI (95%) = 0.44-1.47). Additionally, a descriptive analysis was performed on stranding data collected in French Guiana between 2014 and 2020 to identify the major cause of death and seasonality in the stranding events. In total, 43 dolphins were found, especially on the beaches of Rémire-Montjoly, Cayenne, and Kourou: bycatch was the major identifiable cause of death. We recommend a local conservation strategy and actions to be undertaken in the short- and medium-term to address different issues: knowledge, threats, conservation, and cooperation.

Published
2022

33. G lobal phylogeography of ridley sea turtles (

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

Abstract

Globally distributed marine taxa are well suited for investigations of biogeographic impacts on genetic diversity, connectivity, and population demography. The sea turtle genusThe online version contains supplementary material available at 10.1007/s10592-022-01465-3.

Published
2022

34. 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

35. 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

36. 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
Mammals, Multidisciplinary, Animals, Forests, Artiodactyla
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
2021

37. 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

38. DNA barcoding of the rodent genusOligoryzomys(Cricetidae: Sigmodontinae): mitogenomic-anchored database and identification of nuclear mitochondrial translocations (Numts)

Author

Marcelo Weksler, Alexandra M. R. Bezerra, João Alves de Oliveira, Francisco Prosdocimi, Luiz Flamarion B. Oliveira, Cibele R. Bonvicino, Marcos de O.R. da Cruz, Claudia Regina Silva, Carolina Furtado, Lena Geise, Benoit de Thoisy, François Catzeflis, Universidade Federal do Rio de Janeiro (UFRJ), Museu Paraense Emílio Goeldi [Belém, Brésil] (MPEG), Universidade do Estado do Rio de Janeiro [Rio de Janeiro] (UERJ), 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, and Université de Montpellier (UM)

Subjects
0106 biological sciences, 0301 basic medicine, Mitochondrial DNA, [SDV]Life Sciences [q-bio], Pseudogene, mitochondrial DNA, Biology, computer.software_genre, 010603 evolutionary biology, 01 natural sciences, DNA barcoding, Coalescent theory, 03 medical and health sciences, Genetics, Molecular Biology, Oryzomyini, Oligoryzomys, pseudogenes, Database, Phylogenetic tree, Cytochrome b, [SDV.BA]Life Sciences [q-bio]/Animal biology, coalescent, biology.organism_classification, 030104 developmental biology, computer
Abstract

International audience; DNA barcoding has become a standard method for species identification in taxonomically complex groups. An important step of the barcoding process is the construction of a library of voucher-based material that was properly identified by independent methods, free of inaccurate identification, and paralogs. We provide here a cytochrome oxidase I (mt-Co1) DNA barcode database for species of the genus Oligoryzomys, based on type material and karyotyped specimens, and anchored on the mitochondrial genome of one species of Oligoryzomys, O. stramineus. To evaluate the taxonomic determination of new COI sequences, we assessed species intra/interspecific genetic distances (barcode gap), performed the General Mixed Yule Coalescent method (GMYC) for lineages' delimitation, and identified diagnostic nucleotides for each species of Oligoryzomys. Phylogenetic analyses of Oligoryzomys were performed on 2 datasets including 14 of the 23 recognized species of this genus: a mt-Co1 only matrix, and a concatenated matrix including mt-Co1, cytochrome b (mt-Cytb), and intron 7 of the nuclear fibrinogen beta chain gene (i7Fgb). We recovered nuclear-mitochondrial translocated (Numts) pseudogenes on our samples and identified several published sequences that are cases of Numts. We analyzed the rate of non-synonymous and synonymous substitution, which were higher in Numts in comparison to mtDNA sequences. GMYC delimitations and DNA barcode gap results highlight the need for further work that integrate molecular, karyotypic, and morphological analyses, as well as additional sampling, to tackle persistent problems in the taxonomy of Oligoryzomys.

Published
2019

39. Population structure, phylogeography, and genetic diversity of the common bottlenose dolphin in the tropical and subtropical southwestern Atlantic Ocean

Author

Melina Baumgarten, Lídio França do Nascimento, Daniel Danilewicz, Benoit de Thoisy, Alexandre N. Zerbini, Raquel Almeida, Vitor Luz, Maurício Tavares, Janaína Carrion Wickert, Paulo Henrique Ott, Salvatore Siciliano, Lucas Milmann, Larissa Rosa de Oliveira, Neusa Renata Emin-Lima, Ana Carolina Oliveira de Meirelles, Victor Hugo Valiati, Sandro L. Bonatto, Lúcia D. Fraga, and Fernando Lopes

Subjects
0106 biological sciences, geography, Genetic diversity, geography.geographical_feature_category, Ecology, biology, Range (biology), 010604 marine biology & hydrobiology, Estuary, Subtropics, Parapatric speciation, Bottlenose dolphin, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Phylogeography, Genetics, Animal Science and Zoology, Genetic variability, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation
Abstract

We assessed the level of genetic variability and population structure of the common bottlenose dolphin (Tursiops truncatus) in the tropical and subtropical portions of the southwestern Atlantic Ocean and compared the results with previous morphological findings. We analyzed 109 samples of common bottlenose dolphins that were sequenced for control region mtDNA and genotyped for seven polymorphic microsatellite loci. The results suggested that the species in this region can be separated in two major biological units, northern and southern, with an area of parapatry at southern Brazil. The northern unit seems to occur in a wide range of depths, including offshore waters, is consistent with the canonical morphology of T. truncatus, and can be divided into three management units: 1) Saint Paul’s Rocks, 2) north and northeast of Brazil, and 3) Campos and Santos Basins (that extend at least to southernmost Brazil). The southern unit is coastal, occurring exclusively in very shallow waters (< 10 m) and estuaries, and is consistent with the previously described (putative) Tursiops gephyreus. Nevertheless, a formal decision on the taxonomic status of T. gephyreus should wait for a more geographically comprehensive and data-integrative study.

Published
2019

40. Connecting paths between juvenile and adult habitats in the Atlantic green turtle using genetics and satellite tracking

Author

Bénédicte Chanteur, Myriam Bouaziz, Emmanuel Sutter, Yvon Le Maho, Luc Rangon, Noémie Chanteux, Thomas Maillet, Cédric Frouin, Patrick Queneherve, Nathalie Aubert, Julie Gresser, Céline Murgale, Damien Chevallier, Cyrille Barnerias, Adrien Pinson, Jean-Pierre Allenou, Robinson Bordes, Fabien Lefebvre, Odile Petit, Christelle Guimera, Abdelwahab Benhalilou, Blandine Guillemot, Maïlis Huguin, Christelle Béranger, Fabien Vedie, Émilie Dumont-Dayot, Jordan Martin, Julien Mailles, Nicolas Lecerf, Gaëlle Hiélard, Philippine Chambault, Sidney Régis, Nicolas Cimiterra, Matthieu Duru, Denis Etienne, Benoit de Thoisy, Thierry Woignier, Laurent Thieulle, Marc Bonola, Frédéric Flora, 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, DEAL Martinique, MEDDTL, Office de l'Eau Martinique, Délégation Inter Régionale Outre-mer, Surfrider Foundation Europe, IRD Martinique-Caraïbe (IRD Martinique-Caraïbe), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Association POEMM (Association POEMM), Parc naturel régional de la Martinique (PNR Martinique), and Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU)

Subjects
migration routes, 0106 biological sciences, immature green turtle, location.country, Foraging, Endangered species, Satellite tracking, migration, 010603 evolutionary biology, 01 natural sciences, location, Juvenile, 14. Life underwater, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, Ecology, Evolution, Behavior and Systematics, Original Research, Nature and Landscape Conservation, routes, Chelonia mydas, Ecology, 010604 marine biology & hydrobiology, mixed stock analysis, Exclusive economic zone, Fishery, Geography, Habitat, [SDU]Sciences of the Universe [physics], Martinique island, developmental habitats, [SDE]Environmental Sciences, Martinique
Abstract

International audience; Although it is commonly assumed that female sea turtles always return to the beach they hatched, the pathways they use during the years preceding their first reproduction and their natal origins are most often unknown, as it is the case for juvenile green turtles found in Martinique waters in the Caribbean. Given the oceanic circulation of the Guiana current flowing toward Martinique and the presence of important nesting sites for this species in Suriname and French Guiana, we may assume that a large proportion of the juvenile green turtles found in Martinique are originating from the Suriname-French Guiana beaches. To confirm this hypothesis, we performed mixed stock analysis (MSA) on 40 green turtles sampled in Martinique Island and satellite tracked 31 juvenile green turtles tagged in Martinique to (a) assess their natal origin and (b) identify their destination. Our results from MSA confirm that these juveniles are descendant from females laying on several Caribbean and Atlantic beaches, mostly from Suriname and French Guiana, but also from more southern Brazilian beaches. These results were confirmed by the tracking data as the 10 turtles leaving Martinique headed across the Caribbean-Atlantic region in six different directions and 50% of these turtles reached the Brazilian foraging grounds used by the adult green turtles coming from French Guiana. One turtle left the French Guianan coast to perform the first transatlantic migration ever recorded in juvenile green turtles, swimming toward Guinea-Bissau, which is the most important nesting site for green turtles along the African coast. The extensive movements of the migrant turtles evidenced the crossing of international waters and more than 25 exclusive economic zones, reinforcing the need for an international cooperative network to ensure the conservation of future breeders in this endangered species.

Published
2018

41. Amazonian mammal monitoring using aquatic environmental DNA

Author

Jérôme Murienne, Opale Coutant, Alice Valentini, Cécile Richard-Hansen, Sébastien Brosse, Tony Dejean, Benoit de Thoisy, Régis Vigouroux, and Jean-Baptiste Decotte

Subjects
0106 biological sciences, 0301 basic medicine, Arboreal locomotion, Sampling efficiency, Amazonian, Fauna, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Aquatic species, Genetics, Animals, DNA Barcoding, Taxonomic, Environmental DNA, Transect, Ecology, Evolution, Behavior and Systematics, Mammals, Ecology, Water, Biodiversity, DNA, Environmental, French Guiana, 030104 developmental biology, Geography, Mammal, Species richness, Biotechnology, Environmental Monitoring
Abstract

Environmental DNA (eDNA) metabarcoding has emerged as one of the most efficient methods to assess aquatic species presence. While the method can in theory be used to investigate nonaquatic fauna, its development for inventorying semi-aquatic and terrestrial fauna is still at an early stage. Here we investigated the potential of aquatic eDNA metabarcoding for inventorying mammals in Neotropical environments, be they aquatic, semi-aquatic or terrestrial. We collected aquatic eDNA in 96 sites distributed along three Guianese watersheds and compared our inventories to expected species distributions and field observations derived from line transects located throughout French Guiana. Species occurrences and emblematic mammalian fauna richness patterns were consistent with the expected distribution of fauna and our results revealed that aquatic eDNA metabarcoding brings additional data to line transect samples for diurnal nonaquatic (terrestrial and arboreal) species. Aquatic eDNA also provided data on species not detectable in line transect surveys such as semi-aquatic, aquatic and nocturnal terrestrial and arboreal species. Although the application of eDNA to inventory mammals still needs some developments to optimize sampling efficiency, it can now be used as a complement to traditional surveys.

Published
2020

42. Achieving high-quality ddRAD-like reference catalogs for non-model species: the power of overlapping paired-end reads

Author

Sibelle T. Vilaça, Susan Mbedi, Tomás Carrasco-Valenzuela, Camila J. Mazzoni, Benoit de Thoisy, Felix Heeger, Maximilian Driller, Damien Chevallier, and Larissa Souza Arantes

Subjects
Set (abstract data type), Computer science, Locus (genetics), Single-nucleotide polymorphism, Pairwise comparison, Computational biology, sea turtles, non-model species, RAD pipeline, ddRAD, single copy orthologs, high-throughput sequencing, Genotyping, Genome, Selection (genetic algorithm), Reference genome
Abstract

Reduced representation libraries (RRS) allow large scale studies on non-model species to be performed without the need for a reference genome, by building a pseudo-reference locus catalog directly from the data. However, using closely-related high-quality genomes can help maximize nucleotide variation identified from RRS libraries. While chromosome-level genomes remain unavailable for most species, researchers can still invest in building high-quality and project-specificde novolocus catalogs. Among methods that use restriction enzymes (RADSeq), those including fragment size selection to help obtain the desired number of loci - such as double-digest RAD (ddRAD) - are highly flexible but can present important technical issues. Inconsistent size selection reproducibility across libraries and variable coverage across fragment lengths can affect genotyping confidence, number of identified single nucleotide polymorphisms (SNPs), and quality and completeness of thede novoreference catalog. We have developed a strategy to optimize locus catalog building from ddRAD-like data by sequencing overlapping reads that recreate original fragments and add information about coverage per fragment size. Furtherin silicosize selection and digestion steps limit the filtered dataset to well-covered sets of loci and identity thresholds are estimated based on sequence pairwise comparisons. We have developed a full workflow that identifies a set of reduced-representation single-copy orthologs (R2SCOs) for any given species and that includes estimating and evaluating allelic variation in comparison with SNP calling results. We also show how to use our concept in an established RADSeq pipeline - Stacks - and confirm that our approach increases average coverage and number of SNPs called per locus in the final catalog. We have demonstrated our full workflow using newly generated data from five sea turtle species and provided further proof-of-principle using published hybrid sea turtle and primate datasets. Finally, we showed that a project-specific set of R2SCOs perform better than a draft genome as a reference.

Published
2020

43. De l’animal à l’homme : update sur la fièvre Q et la leptospirose en Amérique latine

Author

Loïc Epelboin, Souza Ribeiro Mioni, M., Saout, M., Vincent Pommier de Santi, Bernard Davoust, Marié, J. L., Destoop, J., Cicuttin, G., Olivier Duron, Benoit de Thoisy, Guillaume Velut, Félix Djossou, Roch, A., Magalie Pierre Demar, Rousset, E., Unité des Maladies Infectieuses et Tropicales [Cayenne, Guyane Française], Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Université de Guyane (UG), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Association Kwata - Etude et protection de la nature [Guyane], Université Paris Descartes - Faculté de Médecine (UPD5 Médecine), Université Paris Descartes - Paris 5 (UPD5), and Unité des Maladies Infectieuses et Tropicales (UMIT)

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2020

44. NEOTROPICAL CARNIVORES: a data set on carnivore distribution in the Neotropics

Author

André Monteiro, Caroline Leuchtenberger, Juliana Monteiro de Almeida-Rocha, José Salatiel Rodrigues Pires, Isabella Oliveira-Bevan, Armando Muniz Calouro, Valquíria Cabral Araújo, María Beatriz Núñez, Donald P. Eaton, Tatiane Campos Trigo, Raquel Lopes Sinigaglia Caribé Grando, Lucas Gonçalves da Silva, Rayanne Gama Matos, Melissa Sanches Mongelli, Larissa Nascimento Barreto, Jorge José Cherem, Paulo Auricchio, Jader Marinho-Filho, Lais Camila Dahmer, Erick Sekiama Rocha, Michel Barros Faria, Leonardo Marques Costa, Claudio Leite Novaes, Fernanda Cristina de Barros, Omolabake Alhambra Silva Arimoro, Ana Paula Potrich, Walfrido Moraes Tomas, Marilia Teresinha Hartmann, Luciana Zago da Silva, Bianca Ingberman, Maíra Benchimol, Ana Maria de Oliveira Paschoal, Fernanda Cavalcanti de Azevedo, Milene Alves-Eigenheer, Jeffrey J. Thompson, Marina Xavier da Silva, Adriele Aparecida Pereira, Beatriz da Silva de Souza Francisco, Michel Schutte, José Clemensou dos Reis Júnior, José de Sousa e Silva Júnior, Ana Cristina Tomazzoni, Milton Cezar Ribeiro, Carolline Zatta Fieker, Shery Duque Pinheiro, Mario Haberfeld, Fabiana Lopes Rocha, Thiago Philipe de Camargo e Timo, Fredy Ramírez Pinto, André Pinassi Antunes, Kevin M. Flesher, Bruno Rodrigo de Albuquerque França, Enrique González, Ricardo Bassini-Silva, Analice Maria Calaça, Patrício Adriano da Rocha, Maximiliano Víctor Pardo, Anamélia de Souza Jesus, Howard Quigley, Ana Paula Nascimento Gomes, Pedro Cordeiro-Estrela, Joana Zorzal Nodari, Cristiano Trapé Trinca, José Hernán Sarasola, Rodrigo Raúl León Pérez, Bruna Silva Santos, Cecília Licarião Luna, Carlos Hass, Elmary da Costa Fraga, Bruno Busnello Kubiak, Samuel Astete, Alexandra Cravino Mol, Alberto Yanosky, Noé U. de la Sancha, Calebe Pereira Mendes, Maurício B. Vecchi, Thiago Ferreira Rodrigues, Camila de Fátima Priante, Maria Emilia Huerta, J. Antonio de la Torre, Matheus Rocha Jorge Corrêa, Carlos Eduardo Verona, Milton José de Paula, Fernando Gonçalves, Ana María Herrera Victoria, Thiago Cavalcante, Eduardo Delgado Britez Rigacci, Viviane Maria Guedes Layme, Francisco Grotta-Neto, Lucas Pacciullio Gaspar, Marcela Guimarães Moreira Lima, Jéssica Abonizio Gouvea, Carlos De Angelo, Fabíola Keesen Ferreira, Juan Ruiz-Esparza, Arthur Francisco Araújo Fernandes, Lucas Lacerda Toth Quintilham, Hiago Ermenegildo, Nivaldo Peroni, Maria João Ramos Pereira, Bruna da Silva Andrade, Juan Pablo Arrabal, Juan F. Charre-Medellín, Geraldo Wilson Fernandes, Daiana Jeronimo Polli, Natália Mundim Tôrres, Samara Arsego Guaragni, Hipólito Ferreira Paulino Neto, Robert Buitenwerf, Rayssa Faria Pedroso, Flávio Kulaif Ubaid, Fernando Pedroni, Allison L. Devlin, Lorena Anne Nascimento, Marcelo Passamani, Mark Bowler, Michael P. Gilmore, Guilherme Zamarian Rezende, João Carlos Zecchini Gebin, Daiane Buscariol, Frederico Gemesio Lemos, Matthew E. Gompper, Paulo de Tarso Zuquim Antas, Rômulo Romeu Nóbrega Alves, Roberto Junior Tomasi, Pablo Villalva, Adriana Bocchiglieri, Rafael Bessa, Marcos de Souza Lima Figueiredo, Lucia Nathaly Stefany Rojas, Darci Moraes Barros-Battesti, Otávio Santi Ribeiro, Paulo Marinho, Francisco Palomares, Camila Cantagallo Devids, Carla Cristina Gestich, Magnus Machado Severo, Fernando de Castro Jacinavicius, Patrícia Kerches Rogeri, Rodrigo Medina Fróes, Fernando Anaguano-Yancha, Marcela Figuerêdo Duarte Moraes, Erick Francisco Aguiar, Átilla Colombo Ferreguetti, Margareth Lumy Sekiama, Mariana Sampaio Xavier, Giselle Bastos Alves, Vinícius Santana Orsini, Gastón Andrés Fernandez Giné, Pietro de Oliveira Scarascia, Leandro Silveira, Juan M. Campos Krauer, Matheus Gonçalves dos Reis, Robert B. Wallace, Fernanda do Passo Ramalho, Lucas Rodrigo Rezende, Flávio Eduardo Vilas Boas, Martín Alejandro Montes, Vinicius A. G. Bastazini, Natalia Mariana Denkiewicz, Fabio Mello Patiu, Galo Zapata-Ríos, Cristiane Martin, Daniel da Silva Ferraz, Ana Elisa de Faria Bacellar, Leonor Valenzuela, Laís Lautenschlager, María Eugenia Iezzi, Geruza Leal Melo, Andrés J. Novaro, Andrea Siqueira Carvalho, Pierre-Cyril Renaud, Ana Priscila Medeiros Olímpio, Renata Alonso Miotto, Alexine Keuroghlian, Anderson Claudino Rolim, Márcio Leite de Oliveira, Mariana M. Vale, Elisabete Rechenberg, Leonardo Henrique da Silva, Maron Galliez, Sávio Augusto de Souza Machado, Martin Buschiazzo, Mateus Melo-Dias, Priscilla de Paula Andrade Cobra, Pamella Gusmão de Goés Brennand, Cristiana Simão Seixas, Diana Friedeberg, Leonardo Sartorello, Paula Cruz, Leandro Santana Moreira, Carlos Frederico Duarte Rocha, Alex Augusto Abreu Bovo, Noeli Zanella, Javier de la Maza, Roberta Montanheiro Paolino, Marina Lima da Silva, Pedro Sarmento, Andrezza Bellotto Nobre, Laura Villalba, Maurício Eduardo Graipel, Paulina Arroyo-Gerala, George V. N. Powell, Rogério Cunha de Paula, Sebastián Andrés Costa, João Paulo Gava Just, Cuauhtémoc Chávez, Daniel H. Thornton, Jonas Sponchiado, Jorge Reppold Marinho, Elildo A.R. Carvalho, Leandro de Oliveira Marques, Rony García-Anleu, Keila Macfadem Juarez, Rafael Reyna-Hurtado, Flávia P. Tirelli, Maria Laura Gomez Vinassa, Jens-Christian Svenning, Frederico Gustavo Rodrigues França, Luiza Neves Guimarães, Maria Augusta Andrade da Silva, Miriam Lucia Lages Perilli, Stefani Gabrieli Age, Clinton N. Jenkins, Joseph E. Hawes, Letícia Benavalli, Akyllam Zoppi Medeiro, André Faria Mendonça, Jose Roberto de Matos, Juliane Pereira-Ribeiro, José Maurício Barbanti Duarte, Maria del Carmen Fleytas Jover, Alberto González-Gallina, Felipe Martello, Eduardo Marques Santos, Marcelo Cervini, Adriano Garcia Chiarello, Erika Castro, Sérgio Lucena Mendes, Wesley Dáttilo, Nilton C. Cáceres, Rodrigo Affonso de Albuquerque Nóbrega, Vlamir José Rocha, Nelson Henrique de Almeida Curi, Javier Hinojosa, Fernando R. Tortato, Rayssa Mainette Nantes Durães, Douglas de Matos Dias, Mauricio Osvaldo Moura, Juliano André Bogoni, Gindomar Gomes Santana, Daniel Galiano, Silvio Junior Napiwoski, Fabiane de Aguiar Pereira, Roberto Fusco-Costa, Samile Seber, Valeria C. Onofrio, Alejandro Jesús de la Cruz, Wellington Hannibal, Maria Brunini Siviero, Henrique Rajão, Nathália Fernandes Canassa, Natalie Olifiers, José Carlos Chaves dos Santos, Eloisa Neves Mendonça, Felipe Pessoa da Silva, Gabriela Heliodoro, Claudia Paola Zárate-Castañeda, Karl Didier, Mariana Bueno Landis, Igor Kintopp Ribeiro, Denise Alemar Gaspar, Marcos Adriano Tortato, Larissa Fornitano, Gabriela Teixeira Duarte, Gabriel Selbach Hofmann, Ana Cristyna Reis Lacerda, Emiliano Guijosa-Guadarrama, Saulo M. Silvestre, Helena Godoy Bergallo, Jardel Brandão Seibert, Sebastián Albanesi, Ariane Teixeira Bertoldi, Juan Andrés Martínez Lanfranco, Jairo Pérez-Torres, José Otávio Venancio, Edeltrudes Maria Valadares Calaça Camara, Fabiano Rodrigues de Melo, Tiberio Cesar Monterrubio, Beatriz de Mello Beisiegel, Eduardo Roberto Alexandrino, Luiz Henrique Medeiros Borges, Raone Beltrão-Mendes, Adriani Hass, João Paulo Villani, Fernando Henrique Puertas, Sara Álvarez Solas, Maria Cristina Peñuela Mora, Andre Monnerat Lanna, Sandra Maria Hartz, Hugo del Castillo, Sônia A. Talamoni, Flávia G. Chaves, Anah Tereza de Almeida Jácomo, Anderson Pagoto, Bruno Leles, Yaribeth Bravata de la Cruz, Brenda Pereira-Silva, Victor Hugo da Silva Iwakami, Juliani Bruna Zanoni, Maísa Ziviani Alves Martins, Claudia Zukeran Kanda, Catalina Sánchez-Lalinde, Marcelo Hideki Yamane, Laura Martins Magalhães, Ailin Gatica, Edson de Souza Lima, Cecilia Cronemberger, Vanessa Tavares Kanaan, Fernando César Gonçalves Bonfim, Italo Mourthe, Taiguã Corrêa Pereira, Igor Pfeifer Coelho, André Chein Alonso, Ludimila Juliele Carvalho-Leite, Felipe Pedrosa, Sean Keuroghlian-Eaton, Paulo Afonso Hartmann, Marcel José Franco Penteado, Pedro Volkmer de Castilho, Henrique Villas Boas Concone, Sérgio Luiz Althoff, Marina Rivero, Andressa Barbara Scabin, Arystene Nicodemo Ferreira, Júlia Beduschi, Marina Zanin, Juan Carlos Rudolf, Jociel Ferreira Costa, Viviana B. Rojas Bonzi, Cauanne Iglesias Campos Machado, Rhayssa Terra de Faria, Ana Cecilia Ochoa, Marcelo Magioli, Renata Twardowsky Ramalho Bonikowski, Ananda de Barros Barban, Natasha Moraes de Albuquerque, Claudia Cristina Cinta, Camila Alvez Islas, Marianela Velilla, Eder Barbier, Jose Luis Cartes, Eduardo Carrano, Glauber Henrique Borges de Oliveira Souto, Carlos Leonardo Vieira, Kimberly Danielle Rodrigues de Morais, Leticia Prado Munhoes, Jana Rangel Silveira, Helio Secco, Fernanda Martins Hatano, Edgar Chávez-González, Marcelo da Silva, Claudia Guimarães Costa, Christine Steiner São Bernardo, Ubiratan Piovezan, Paula Ribeiro Prist, Victor Vale, Elvira D'Bastiani, Juan L. Peña-Mondragón, Micheli Ribeiro Luiz, Eduardo Eizirik, Ana Raíssa Cunha Costa, Rodrigo de Almeida Nobre, Heitor Miraglia Herrera, Maria Elisa de Freitas Morandi, Valeria Towns, Danielle de Oliveira Moreira, Robson Odeli Espíndola Hack, Maria Claudene Barros, Adriano Pereira Paglia, Marinêz Isaac Marques, Carlos César Durigan, Marcia Maria de Assis Jardim, Rodrigo Paulo da Cunha Araújo, Erika de la Peña-Cuéllar, Rafael Cerqueira Castro de Souza, Emiliano Esterci Ramalho, Carlos Henrique Salvador, Maria Emília de Avelar Fernandes, Marcus Vinícius Vieira, Laís Aline Grossel, Martha Lucia Ortiz-Moreno, Renata L. Muylaert, John Polisar, Sixto Fernández Ramirez, Rômulo Theodoro Costa, Fabiane Girardi, Julio Chacón Pacheco, Gabriel Lima Aguiar, Ronaldo Gonçalves Morato, Leonardo Siqueira Mendonça, Roberto Guilherme Trovati, Camila Moniz Freire Rodrigues, David Costa Braga, Nielson Pasqualotto, Evellyn Borges de Freitas, Edvandro Abreu Ribeiro, German Forero-Medina, Adauto de Souza Ribeiro, Tayana Mendonça da Silva Gondim, Vivian da Silva Braz, Mariana Guenther, Beatriz Azevedo Cezila, Diego J. Lizcano, Daniele Janina Moreno, Caryne Braga, Agnis Cristiane de Souza, Ednaldo Cândido Rocha, Maira Giuliana Quatrocchi, Rubén Cueva Loachamin, Ricardo Sampaio, Rafael Spilere Romagna, Larissa de Nazaré Barros Barbosa, Pedro Luna, Ramonna de Oliveira, Marcela Alvares Oliveira, Lívia Maria de Paula, Valeska Buchemi Oliveira, Rugieri Juárez, Marcella do Carmo Pônzio, Karl L. Schuchmann, Erich Fischer, Juliana Jordao, André Luis Botelho de Moura, Pedro M. Galetti, Luciano Martins Verdade, Bruno Augusto Torres Parahyba Campos, Newton Mota Gurgel-Filho, Luiz Henrique Lyra, Ana Kellen Nogueira Campelo, Kamila Marianne Contreras Palma, Fernanda Santos, Vanessa Lazaro Melo, Graziele Oliveira Batista, Camilla Angélica de Lima, Antonio M. Mangione, Nereyda Falconi, Camila Camara Pianca, Alessandra Bertassoni, Waldney Pereira Martins, Anderson Feijó, Santiago Espinosa, André Luís Luza, Lana Resende de Almeida, Bruna Bertagni de Camargo, Rogério Parentoni Martins, Rita de Cassia Bianchi, Julia Carolina Mata, Fabio Rohe, Marcos Silveira, Pedro Henrique de Faria Peres, Diego Carvalho Viana, Renata R. D. Chagas, Andiara Silos Moraes de Castro e Souza, Felipe Vélez-García, Felipe Bittioli Rodrigues Gomes, Alan Eriksson, José A. Rodríguez-Pulido, Maria Estela Viscarra Siñani, Davi Castro Tavares, João Pedro Souza-Alves, Raquel da Silva, Lucas Ramis Segura, Amadeo Sánchez, João M. D. Miranda, Natani Da Silva De Lima, Antonio Millas Silva Pinto, Wesley Rodrigues Silva, Jörn Ziegler, Lilian Catenacci, Mauro Galetti, Tainah Cruz Moreira, Cristiane Patricia Zaniratto, Danilo Augusto Farias, Anna Carolina Figueiredo de Albuquerque, Lilian Elaine Rampim, Caroline Charão Sartor, Maria Luisa S. P. Jorge, Alex Bager, Maria Lucia Lorini, Rodolfo Assis Magalhães, Rodrigo Lima Massara, Juliana Silveira dos Santos, Vagner Cavarzere, Cíntia M. Lopes, Greici Maia Behling, Fernanda Delborgo Abra, Fabricio Diaz-Santos, Helena Alves do Prado, Daniela Lamattina, Rubia Santana Andrade, Kathrin Burs, Ramon Lima Silva, Meyline de Oliveira Souza Almeida, José Fernando Moreira Ramírez, Maria Cristina Ferreira do Rosario, Franco L. Souza, Maria Santina de Castro Morini, Ana Carla Medeiros Morato de Aquino, Mauricio Neves Godoi, Marcelo Alejandro Villegas, Paulo Inácio Prado, Mariano Maudet Bergel, Gustavo Alves da Costa Toledo, Ângela Camila Deffaci, Diogo Loretto, Diego Afonso Silva, Henrique Llacer Roig, Richard Hatakeyama, Mario S. Di Bitetti, Carmen Elena Barragán Ruiz, Alexandra M. R. Bezerra, Flávio Henrique Guimarães Rodrigues, Fernanda Michalski, Jasmine de Resende Assis, Jose Milton Longo, Paula Sanches Martin, Murillo Prado da Silva, Pablo Rodrigues Gonçalves, Daiane Cristina Carreira, Andrea Dechner, Carolina Carvalho Cheida, Gabrielle Beca, Hugo Fernandes-Ferreira, Ricardo Araújo Pires, Alfonso Zúñiga Hartley, Hugo Cabral, Luiz Flamarion B. Oliveira, Renato R. Hilário, Samanta Uchôa Bordallo, Fernando C. Passos, Herbert Duarte, Fabio de Oliveira Roque, Fabio Oliveira do Nascimento, Fábio Soares, Alexandre Reis Percequillo, Emiliana Isasi-Catalá, Manoel Rodrigues, Clarissa Alves da Rosa, Marcelo Augusto dos Santos Junior, José Eduardo Mantovani, Andressa Gatti, Saulo Ramos Lima, Laury Cullen, Erica Naomi Saito, Carlos A. Peres, Caroline Espinosa, Guido Marcos Ayala Crespo, Leticia Coutinho Sangy Dias, Jean Paul Metzger, Paulo H. S. A. Camargo, Ana Carolina Srbek-Araujo, Christine Del Vechio, Olivier Pays, Júlia Emi de Faria Oshima, Ludmila Hufnagel, Diego Astúa, Renan Lieto Alves Ribeiro, Katia Maria Paschoaletto Micchi de Barros Ferraz, Mircea G. Hidalgo-Mihart, Octavio Monroy-Vilchis, Lucas Neves Perillo, Cindy M. Hurtado, Cristina Jaques da Cunha, Rony Peterson Santos Almeida, Jasmim Felipe Oliveira, Leonardo dos Santos Aguiar, Antonio Rossano Mendes Pontes, Nêmora Pauletti Prestes, Felipe Moreli Fantacini, Sérgio Bazilio, Isabel Melo, Glenda Jéssica Villarroel, Rafael Hoogesteijn, Lilian Bonjorne, Luis Renato Rezende Bernardo, Maurício Quoos Konzen, Juan Ignacio Zanón-Martínez, Paloma Marques Santos, Whaldener Endo, Diego Varela, Benoit de Thoisy, Karla Chávez-Congrains, Yuri Geraldo Gomes Ribeiro, Jaime Xavier Palacios Perez, Mariana Silva Tavares, Fernando M. Contreras-Moreno, Luciano Carramaschi de Alagão Querido, Francesca Belem Lopes Palmeira, Bianca dos Santos Neves, José Luis Passos Cordeiro, Erik Daniel Martínez Nambo, Mariane da Cruz Kaizer, João Luiz Rossi Junior, Mauricio M. Núñez-Regueiro, José Oliveira Dantas, Cristina Fabiola López-Fuerte, Giordano Ciocheti, Marina Salles Munerato, Eleonore Z. F. Setz, Júlia Ilha, Karen Giselle Rodriguez Castro, Mozart C. Freitas-Junior, André Luiz Ferreira da Silva, Eduardo Martins Venticinque, Vilmar Picinatto Filho, Francys E. da Veiga da Costa, Renata Valls Pagotto, Cyntia Cavalcante Santos, Carla Denise Tedesco, Julia Camara Assis, Raphaella Coutinho, Luciana Souza Araújo, João Gabriel Ribeiro Giovanelli, Jesus R.D. Souza, Mariana B. Nagy-Reis, Joedison Rocha, Luiz Gustavo Rodrigues Oliveira Santos, André Valle Nunes, Andiara Paula Hermann, Samia E. Carrillo-Percastegui, Lucy Perera-Romero, Ingridi Camboim Franceschi, Filipe Martins Santos, Itiberê P. Bernardi, Érica Hasui, Joyce Gonçalves Santos, Paula Modenesi Ferreira, Thamíris Christina Karlovic, María Celina Carrizo, Marília A. S. Barros, Almir de Paula, Carlos Benhur Kasper, Guilherme Mourão, Mathias W. Tobler, Camilo Ribeiro de Lima, Paulo Wesley Martins, Jamile de Moura Bubadué, João Paulo Pandini Favoretti, William Bercê, Leonardo de Paula Gomes, Leonardo C. Oliveira, Diogo Maia Gräbin, Gabrielle Ribeiro de Andrade, Rodrigo Bernardo, Thiago Bernardes Maccarini, Carlos Eduardo Fragoso, Rafaela Aparecida da Silva, Viviane Telles Rodrigues Gaboardi, Raony de Macêdo Alencar, Fernanda Guedes da Silva, Anelise Montanarin, Vinicius Rodrigues Tonetti, Bruno H. Saranholi, Larissa L. Bailey, Martin Roberto Del Valle Alvarez, Juliana Bonanomi, Paula Akkawi, Vinicius Alberici, Grasiela Edith de Oliveira Porfírio, Adriano Canteri, Jimmy Pincheira-Ulbrich, Alan N. Costa, Fabio Gabriel Díaz-Santos, Douglas Machado da Silva, Ezequiel Pedó, Lucía Martínez Retta, Alvaro García-Olaechea, Ricardo Sartorello, Paulo Henrique Peira Ruffino, Alexandre Martins Costa Lopes, Crizanto Brito De-Carvalho, Eliana César Laranjeira Duarte Rocha, Karen B. Strier, Raylenne da Silva Araujo, Jaime Martinez, Augusto Lisboa Martins Rosa, Eduardo Nakano-Oliveira, Rodrigo Silva Pinto Jorge, Hudson de Macedo Lemos, Aureo Banhos, Pryscilla Moura Lombardi, Alexandre Vogliotti, Rafael Souza Cruz Alves, Mayara Guimarães Beltrão, Carlos Fonseca, Rogério Grassetto Teixeira da Cunha, Nagy-Reis M., Oshima J. E. de F., Zukeran Kanda C., Palmeira F. B. L., Melo F. R. de, Morato R. G., Bonjorne L., Magioli M., Leuchtenberger C., Rohe F., Lemos F. G., and Cravino Mol María Alexandra, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Ecología y Ciencias Ambientales.

Subjects
0106 biological sciences, carnivores, Ecological health, predator, canidae, Roadkill, Species distribution, Carnivora, Mustelidae, mammal, occurrence, 010603 evolutionary biology, 01 natural sciences, data paper, Landscape Architecture and Spatial Planning, Animals, Humans, Carnivore, Ecology, Evolution, Behavior and Systematics, Ecosystem, Trophic level, Canidae, biology, Ecology, 010604 marine biology & hydrobiology, Landschapsarchitectuur en Ruimtelijke Planning, conservation, felidae, biology.organism_classification, Geography, Habitat, neotropical region, species distribution, Ursidae, Count data
Abstract

Incluye contenido parcial de los autores Abstract.Mammalian carnivores are considered a key group in maintaining ecologicalhealth and can indicate potential ecological integrity in landscapes where they occur. Carni-vores also hold high conservation value and their habitat requirements can guide managementand conservation plans. The order Carnivora has 84 species from 8 families in the Neotropicalregion: Canidae; Felidae; Mephitidae; Mustelidae; Otariidae; Phocidae; Procyonidae; andUrsidae. Herein, we include published and unpublished data on native terrestrial Neotropicalcarnivores (Canidae; Felidae; Mephitidae; Mustelidae; Procyonidae; and Ursidae). NEOTRO-PICAL CARNIVORES is a publicly available data set that includes 99,605 data entries from35,511 unique georeferenced coordinates. Detection/non-detection and quantitative data wereobtained from 1818 to 2018 by researchers, governmental agencies, non-governmental organi-zations, and private consultants. Data were collected using several methods including cameratrapping, museum collections, roadkill, line transect, and opportunistic records. Literature(peer-reviewed and grey literature) from Portuguese, Spanish and English were incorporated inthis compilation. Most of the data set consists of detection data entries (n=79,343; 79.7%) butalso includes non-detection data (n=20,262; 20.3%). Of those, 43.3% also include count data(n=43,151). The information available in NEOTROPICAL CARNIVORES will contribute tomacroecological, ecological, and conservation questions in multiple spatio-temporal perspec-tives. As carnivores play key roles in trophic interactions, a better understanding of their distri-bution and habitat requirements are essential to establish conservation management plans andsafeguard the future ecological health of Neotropical ecosystems. Our data paper, combinedwith other large-scale data sets, has great potential to clarify species distribution and relatedecological processes within the Neotropics. There are no copyright restrictions and no restric-tion for using data from this data paper, as long as the data paper is cited as the source of theinformation used. We also request that users inform us of how they intend to use the data.

Published
2020

45. Rodent-borne viruses in French Guiana

Author

Anne, Lavergne, Séverine, Matheus, François, Catzeflis, Damien, Donato, Vincent, Lacoste, and Benoit, de Thoisy

Abstract

Among mammals, rodents play a key role in the emergence of viral diseases. In French Guiana, with 36 rodent species recorded in various ecosystems (pristine forests, savannas, anthropized environments), some natural habitats today encounter anthropogenic perturbations that induce changes in community structure and population dynamics. These modifications are sometimes associated with the circulation and emergence of viral pathogens. For 10 years, investigations on the circulation of two rodent-borne viruses, Hantavirus and Mammarenavirus, are underway in rodent populations as well as in humans for hantavirus. These investigations identified viruses from both genera in their potential reservoirs and allow describing the most favourable habitats for the reservoirs of hantavirus where the risk of viral emergence may be higher. We suggest to investigate how anthropic perturbations in rodent communities can drive the emergence of viruses that are currently confined to a small scale and search for evidence of infection in the human population.

Published
2020

46. 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

47. 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

48. 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

49. How Social Structure Drives the Population Dynamics of the Common Vampire Bat (Desmodus rotundus, Phyllostomidae)

Author

Álvaro Aguilar Setién, Mailis Huguin, Benoit de Thoisy, Claudia Regina Silva, Anne Lavergne, Arielle Salmier, Nidia Aréchiga-Ceballos, Vincent Lacoste, Marguerite Delaval, Amandine Guidez, Isai Jorge de Castro, 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), Association Kwata (Kwata), Kwata, Instituto de Diagnóstico y Referencia Epidemiológicos, Office National des Forêts [Cayenne], Instituto de Pesquisas Científicas e Tecnológicas do Estado do Amapá (IEPA), Estado do Amapa, Instituto Mexicano del Seguro Social [Mexico City, Mexico] (IMSS), Supported by Kwata NGO, Institut Pasteur de la Guyane, DEAL Guyane, and Collectivité Territoriale de la Guyane., All field volunteers and owners and/or managers of capture sites are warmly acknowledged for their assistance in captures. In compliance with Advantages and Benefits Sharing policy in French Guiana, samples are kept in the tissue collection JAGUARS (http://kwata.net/la-collection-jaguars-pour-l-etude-de-la-biodiversite.html, and CITES reference: FR973A)

Subjects
Male, 0106 biological sciences, 0301 basic medicine, Disease reservoir, 01 natural sciences, MESH: Rabies/transmission, Chiroptera, population dynamics, MESH: Chiroptera/virology, MESH: Disease Reservoirs/virology, MESH: Animals, Genetics (clinical), education.field_of_study, MESH: Chiroptera/physiology, biology, sociality, vampire bat, French Guiana, Female, Brazil, Biotechnology, Rabies, Wahlund effect, Population, MESH: Rabies/virology, Zoology, Desmodus rotundus, 010603 evolutionary biology, MESH: Rabies virus/physiology, 03 medical and health sciences, MESH: Chiroptera/genetics, MESH: French Guiana, Genetics, Animals, MESH: Social Behavior, structure, Social Behavior, education, Mexico, MESH: Mexico, Molecular Biology, Disease Reservoirs, Isolation by distance, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], MESH: Population Dynamics, biology.organism_classification, parasite spreading, MESH: Male, 030104 developmental biology, Rabies virus, Vampire bat, Biological dispersal, Philopatry, MESH: Brazil, MESH: Female
Abstract

International audience; Social systems are major drivers of population structure and gene flow, with important effects on dynamics and dispersal of associated populations of parasites. Among bats, the common vampire bat (Desmodus rotundus) has likely one of the most complex social structures. Using autosomal and mitochondrial markers on vampires from Mexico, French Guiana, and North Brazil, from both roosting and foraging areas, we observed an isolation by distance at the wider scale and lower but significant differentiation between closer populations (

Published
2017

50. How to detect an elusive aquatic mammal in complex environments? A study of the Endangered Antillean manateeTrichechus manatus manatusin French Guiana

Author

Virginie Dos Reis, Benoit de Thoisy, and Delma Nataly Castelblanco-Martínez

Subjects
0106 biological sciences, Side-scan sonar, biology, Range (biology), Ecology, 010604 marine biology & hydrobiology, Endangered species, 010603 evolutionary biology, 01 natural sciences, Fishery, Geography, Habitat, Abundance (ecology), biology.animal, Manatee, Aquatic mammal, Mammal, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation
Abstract

The Antillean manateeTrichechus manatus manatusis a cryptic mammal that inhabits, among other areas, murky rivers and estuaries of Central and South America. The difficulty in detecting and counting manatees is an obstacle to monitoring their population status, as traditional count sampling is unsuitable. We conducted a quantitative analysis of the distribution and abundance of the manatee across its known range in the rivers and estuaries of French Guiana, based on data from a range-wide line transect visual survey combined with a side-scan sonar survey, identification of feeding sites, and silent observations at fixed points. A total effective effort of 248 hours and 1,129 km of boat survey was completed. We used two relative abundance indices: the combined encounter rate, which combines encounters per km from either visual or side-scan sonar surveys, and the global detection index, which is defined as the sum of all evidence per unit time. Manatees were detected in all nine study units. Niche modelling was used to analyse the space selection by manatees, and helped to detect differential use of habitats according to the season. The model predicted that coastal areas are used more extensively during the dry season. In the absence of better techniques to detect wild manatees in complex habitats this monitoring protocol may be relevant and replicable in hydrological systems where manatee detectability is constrained by biogeographical characteristics.

Published
2017

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