DNA Barcoding of Sigmodontine Rodents: Identifying Wildlife Reservoirs of Zoonoses

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.

Rodents of the eastern and western slopes of the Tropical Andes: phylogenetic and taxonomic insights using DNA barcodes

“…We also recovered Oligoryzomys as paraphyletic, but we propose that this may be due to two artifacts: incorrect identifications of various voucher specimens associated with sequences available in GenBank (sequences of specimen MN71255 [GenBank accession number: KF815407] ( Figure 4C) actually belongs to Necromys lasiurus, based on the analysis of CYTB of the same specimen,results not shown); and putative pseudogenes (Numts; Bensasson et al 2001) in sequences generated by Müller et al (2013) [GenBank accession numbers: GU938877, GU938878, GU938886-GU938890, GU938892-GU938894, GU938898, GU938899, GU938953, GU938969-GU938988] (Figure 4A), based on the position of these sequences in an analyses of a larger dataset of Oligoryzomys barcodes (M. Weksler et al, in prep.). Traditionally, the genus Oligorzomys has been a hard group to study because of the availability of a large number of taxonomic names and various difficulties inherent in assessing patterns of morphological variation.…”

Range extension for Drymoreomys albimaculatus Percequillo,&nbsp;Weksler &amp; Costa, 2011 (Mammalia, Rodentia, Cricetidae) in Mixed&nbsp;Ombrophilous Forest of southern Brazil with the first occurrence&nbsp;from the state of Paran&aacute;

“…Because it is a newly discovered species, much remains unknown about it, including its natural history, ecology, limits of geographical distribution, phylogeny, and phylogeography (Patton et al 2015). However, cytogenetic studies have been undertaken by Suarez-Villota et al (2013) and Delciellos et al (2015), as well as taxonomic studies, based on DNA barcoding, by Müller et al (2013). Herein, we report the presence of D. albimaculatus at a new location in the state of Santa Catarina and provide the first record from the state of Paraná…”

Does the widely distributed rodent Calomys tener (Cricetidae: Sigmodontinae) constitute a single evolutionary unit?

“…1, Table 1). The five sequences of the COI gene were published by Müller et al (2013). Of the Cyt-b sequences, 19 were published in different studies listed in Table 1, whereas 12 were generated at the lab of Jorge Salazar-Bravo (Texas Tech University, Lubbock, Texas, USA) from samples obtained on loan from several institutions (see Acknowledgements).…”