RESUMO
Characterizing biodiversity is one of the main challenges for the coming decades. Most diversity has not been morphologically described, and barcoding is now complementing morphological-based taxonomy to further develop inventories. Both approaches have been cross-validated at the level of species and OTUs. However, many known species are not listed in reference databases. One path to speed up inventories using barcoding is to directly identify individuals at coarser taxonomic levels. We therefore studied in barcoding of plants whether morphological-based and molecular-based approaches are in agreement at genus, family and order levels. We used Agglomerative Hierarchical Clustering (with Ward, Complete and Single Linkage) and Stochastic Block Models (SBM), with two dissimilarity measures (Smith-Waterman scores, kmers). The agreement between morphological-based and molecular-based classifications ranges in most of the cases from good to very good at taxonomic levels above species, even though it decreases when taxonomic levels increase, or when using the tetramer-based distance. Agreement is correlated with the entropy of morphological-based classification and with the ratio of the mean within- and mean between-groups dissimilarities. The Ward method globally leads to the best agreement, whereas Single Linkage can show poor behaviours. SBM provides a useful tool to test whether or not the dissimilarities are structured by the botanical groups. These results suggest that automatic clustering and group identification at taxonomic levels above species are possible in barcoding.
Assuntos
Código de Barras de DNA Taxonômico , Árvores , Biodiversidade , Análise por Conglomerados , Código de Barras de DNA Taxonômico/métodos , Guiana Francesa , Humanos , Filogenia , Árvores/genéticaRESUMO
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.
Assuntos
Animais Selvagens , Demografia , Ecossistema , Doenças Transmitidas por Vetores , Zoonoses , Animais , Guiana Francesa/epidemiologia , Atividades Humanas , Humanos , Incidência , Pesquisa Interdisciplinar , Prevalência , Doenças Transmitidas por Vetores/epidemiologia , Doenças Transmitidas por Vetores/transmissão , Zoonoses/epidemiologia , Zoonoses/etiologia , Zoonoses/transmissãoRESUMO
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.