Four types of samples were selected in this study. Firstly, 265 high quality tissue samples preserved in ethanol were used as references. They had been collected in Asia, Africa and Europe from rodents that were unambiguously identified at the species level by specialists, based on either morphological characters or molecular data (www.ceropath.org; www.bdrss.ird.fr/bdrsspub_form.php; [55] ). Specimens were selected in order to maximize the number of species and various geographic locations. The total reference sample comprised 103 species, 38 genera and 8 families. In addition, this reference set included closely related species and cryptic species that were only recently described (e.g. species of the Rattus rattus complex, Microtus complex, Gerbillus complex, etc.).
Secondly, 555 samples preserved in ethanol but with uncertain taxonomic status were selected. Feces found in the traps were collected at the same time in order to compare results obtained using high quality DNA (from tissue) or poor quality DNA (from non-invasive samples). Tissue and fecal samples were obtained for 11 and 38 rodents from Mali and Thailand respectively.
Thirdly, 54 DNAs were extracted from museum specimens (skins) and kindly provided by the MNHN of Paris.
And finally, feces from predators that were likely to have ingested rodents were collected. Feces thought to have originated from four foxes (Vulpes vulpes), four martens (Martes martes) and four wild cats (Felis silvestris), as well as 11 owl pellets were analyzed to determine their rodent diets. Sample information is detailed in Table S1.
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