Forêts tropicales, changements d'usage des sols et risques infectieux émergents

Les forêts intertropicales constituent une source exceptionnelle de diversité biologique spécifique en macro-organismes, mais elles se révèlent être aussi de véritables pépinières en micro-organismes. Ces cinquante dernières années, certains de ces micro-organismes, à l'origine présents chez des animaux forestiers ou hébergés dans l'environnement comme le sol ou l'eau, se sont dévoilés être des agents pathogènes plus ou moins sévères pour les populations humaines exposées. Dans cet article, nous discutons des interactions hôtes-micro-organismes rencontrées dans les forêts primaires en les abordant tant d'un angle macroécologique que d'un point de vue plus fonctionnel, en l'illustrant de quatre exemples d'agents microbiens émergents. Plus que tout autre déterminant, les modifications d'usages des sols, notamment au travers de la déforestation pour le développement d'une agriculture, et les contacts avec les micro-organismes via la biodiversité, particulièrement lors de la pratique de chasse, exposent des individus susceptibles à ces nouveaux dangers micro-biens. Avec la déforestation et des expositions croissantes avec la faune sauvage, le risque de nouvelles infections humaines devient une réalité internationale exigeant de la part des autorités publiques de mieux prendre en considération ces éléments pour la sécurité sanitaire mondiale

A new species of tapir from the Amazon

All known species of extant tapirs are allopatric: 1 in southeastern Asia and 3 in Central and South America. The fossil record for tapirs, however, is much wider in geographical range, including Europe, Asia, and North and South America, going back to the late Oligocene, making the present distribution a relict of the original one. We here describe a new species of living Tapirus from the Amazon rain forest, the 1st since T. bairdii Gill, 1865, and the 1st new Perissodactyla in more than 100 years, from both morphological and molecular characters. It is shorter in stature than T. terrestris (Linnaeus, 1758) and has distinctive skull morphology, and it is basal to the clade formed by T. terrestris and T. pinchaque (Roulin, 1829). This highlights the unrecognized biodiversity in western Amazonia, where the biota faces increasing threats. Local peoples have long recognized our new species, suggesting a key role for traditional knowledge in understanding the biodiversity of the region

Population history, phylogeography, and conservation genetics of the last Neotropical mega-herbivore, the lowland tapir (Tapirus terrestris)

<p>Abstract</p> <p>Background</p> <p>Understanding the forces that shaped Neotropical diversity is central issue to explain tropical biodiversity and inform conservation action; yet few studies have examined large, widespread species. Lowland tapir (<it>Tapirus terrrestris</it>, Perissodactyla, Tapiridae) is the largest Neotropical herbivore whose ancestors arrived in South America during the Great American Biotic Interchange. A Pleistocene diversification is inferred for the genus <it>Tapirus </it>from the fossil record, but only two species survived the Pleistocene megafauna extinction. Here, we investigate the history of lowland tapir as revealed by variation at the mitochondrial gene Cytochrome <it>b</it>, compare it to the fossil data, and explore mechanisms that could have shaped the observed structure of current populations.</p> <p>Results</p> <p>Separate methodological approaches found mutually exclusive divergence times for lowland tapir, either in the late or in the early Pleistocene, although a late Pleistocene divergence is more in tune with the fossil record. Bayesian analysis favored mountain tapir (<it>T. pinchaque</it>) paraphyly in relation to lowland tapir over reciprocal monophyly, corroborating the inferences from the fossil data these species are sister taxa. A coalescent-based analysis rejected a null hypothesis of allopatric divergence, suggesting a complex history. Based on the geographic distribution of haplotypes we propose (<it>i</it>) a central role for western Amazonia in tapir diversification, with a key role of the ecological gradient along the transition between Andean subcloud forests and Amazon lowland forest, and (<it>ii</it>) that the Amazon river acted as an barrier to gene flow. Finally, the branching patterns and estimates based on nucleotide diversity indicate a population expansion after the Last Glacial Maximum.</p> <p>Conclusions</p> <p>This study is the first examining lowland tapir phylogeography. Climatic events at the end of the Pleistocene, parapatric speciation, divergence along the Andean foothill, and role of the Amazon river, have similarly shaped the history of other taxa. Nevertheless further work with additional samples and loci is needed to improve our initial assessment. From a conservation perspective, we did not find a correspondence between genetic structure in lowland tapir and ecogeographic regions proposed to define conservation priorities in the Neotropics. This discrepancy sheds doubt into this scheme's ability to generate effective conservation planning for vagile species.</p

COIL: a methodology for evaluating malarial complexity of infection using likelihood from single nucleotide polymorphism data.

International audienceComplex malaria infections are defined as those containing more than one genetically distinct lineage of Plasmodium parasite. Complexity of infection (COI) is a useful parameter to estimate from patient blood samples because it is associated with clinical outcome, epidemiology and disease transmission rate. This manuscript describes a method for estimating COI using likelihood, called COIL, from a panel of bi-allelic genotyping assays. COIL assumes that distinct parasite lineages in complex infections are unrelated and that genotyped loci do not exhibit significant linkage disequilibrium. Using the population minor allele frequency (MAF) of the genotyped loci, COIL uses the binomial distribution to estimate the likelihood of a COI level given the prevalence of observed monomorphic or polymorphic genotypes within each sample. COIL reliably estimates COI up to a level of three or five with at least 24 or 96 unlinked genotyped loci, respectively, as determined by in silico simulation and empirical validation. Evaluation of COI levels greater than five in patient samples may require a very large collection of genotype data, making sequencing a more cost-effective approach for evaluating COI under conditions when disease transmission is extremely high. Performance of the method is positively correlated with the MAF of the genotyped loci. COI estimates from existing SNP genotype datasets create a more detailed portrait of disease than analyses based simply on the number of polymorphic genotypes observed within samples. The capacity to reliably estimate COI from a genome-wide panel of SNP genotypes provides a potentially more accurate alternative to methods relying on PCR amplification of a small number of loci for estimating COI. This approach will also increase the number of applications of SNP genotype data, providing additional motivation to employ SNP barcodes for studies of disease epidemiology or control measure efficacy. The COIL program is available for download from GitHub, and users may also upload their SNP genotype data to a web interface for simple and efficient determination of sample COI

Evidence of cryptic lineages within a small South American crocodilian: the Schneider’s dwarf caiman Paleosuchus trigonatus (Alligatoridae: Caimaninae)

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

Coxiella burnetii Infection in Livestock, Pets, Wildlife, and Ticks in Latin America and the Caribbean: a Comprehensive Review of the Literature

Purpose of the Review Q fever , a bacterial zoonosis caused by Coxiella burnetii, is reported very heterogeneously in humans in Latin America. The objective of this study was to review the data on Coxiella burnetii Infection in animals in Latin America and the Caribbean. Recent Findings A comprehensive literature review was carried out in the 47 countries and territories of Latin America on various search engines and grouped into four groups: livestock, pets, wildlife, and ticks. Summary Thus, 113 studies were selected between 1950 and 2022. Among the 47 countries, only 25 (53%) had at least one publication related to C. burnetii infection in animals. The most productive country was Brazil (N = 51), followed by French Guiana (N = 21), and Colombia (N = 16). Studies in livestock from 20 countries have shown widely varying country-to-country rates of seroprevalence, ranging from 0 to 67%. Some studies from seven countries, especially French Guiana and Brazil, found antibodies and sometimes positive PCR in dogs and cats, generally in the context of investigations around human clustered cases. Knowledge remained fragmented about infection in wildlife from only five countries (Chile, Colombia, Brazil, French Guiana, and Uruguay). C. burnetii infection was identified by PCR in Chiroptera (7 species), Rodentia (6 species), Suina (2 species), Xenartha (1 species), Cingulata (1 species), and Perissodactyla (1 species). Studies on Coxiella sp. in ticks have been performed in 11 countries, mostly in Brazil, and mainly found Coxiella-like endosymbionts. Thus, data on C. burnetii infection in animals are sparse and incomplete in Latin America and the Caribbean, and more research is warranted

Large-scale population disappearances and cycling in the white-lipped peccary, a tropical forest mammal.

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