Abstract
Species identification through DNA barcoding is a tool to be added to taxonomic procedures, once it has been validated. Applying barcoding techniques in public health would aid in the identification and correct delimitation of the distribution of rodents from the subfamily Sigmodontinae. These rodents are reservoirs of etiological agents of zoonoses including arenaviruses, hantaviruses, Chagas disease and leishmaniasis. In this study we compared distance-based and probabilistic phylogenetic inference methods to evaluate the performance of cytochrome c oxidase subunit I (COI) in sigmodontine identification. A total of 130 sequences from 21 field-trapped species (13 genera), mainly from southern Brazil, were generated and analyzed, together with 58 GenBank sequences (24 species; 10 genera). Preliminary analysis revealed a 9.5% rate of misidentifications in the field, mainly of juveniles, which were reclassified after examination of external morphological characters and chromosome numbers. Distance and model-based methods of tree reconstruction retrieved similar topologies and monophyly for most species. Kernel density estimation of the distance distribution showed a clear barcoding gap with overlapping of intraspecific and interspecific densities < 1% and 21 species with mean intraspecific distance < 2%. Five species that are reservoirs of hantaviruses could be identified through DNA barcodes. Additionally, we provide information for the description of a putative new species, as well as the first COI sequence of the recently described genus Drymoreomys. The data also indicated an expansion of the distribution of Calomys tener. We emphasize that DNA barcoding should be used in combination with other taxonomic and systematic procedures in an integrative framework and based on properly identified museum collections, to improve identification procedures, especially in epidemiological surveillance and ecological assessments.
Highlights
Molecular identification of pathogens, their vectors, and their reservoirs is one of the expected applications of the DNA barcoding initiative
In the Bayesian inference (BI) and Maximum likelihood (ML) inferences, Calomys and Delomys were monophyletic, whereas in the NJ tree, Calomys grouped with Rhagomys
At least with respect to sigmodontine rodents and hantaviruses, instead of applying wide-ranging automated methods, taxon-specific discussions could improve our understanding of the potential pitfalls in identification procedures
Summary
Their vectors, and their reservoirs is one of the expected applications of the DNA barcoding initiative. Knowledge of the exact species that is (are) carrying harmful pathogens is essential to studies of the factors leading to occurrences [1,2], pathogen proliferation [3], and transmission between animal vectors [4,5,6], as well as for epidemiological inferences as a whole Worldwide initiatives such as the International Barcode of Life (iBOL) project, taxon-specific projects, and national funding programs have fostered the accumulation of massive standardized sequence data for the cytochrome oxidase c gene (COI), which has contributed significantly to species identification [7,8,9,10,11,12]. The extent to which this approach is useful in specific taxonomic groups is a matter for empirical evaluation
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