Classification in Mindomys
In 2006, Marcelo Weksler published a large-scale cladistic analysis of Oryzomyini ("rice rats"), the group (tribe) to which hammondi and the related species mentioned above belong. He used both morphological and molecular characters, but had only morphological data for Oryzomys hammondi. The placement of the species in his results was unstable; some trees placed it close to the tree rice rats, Oecomys, within clade B and others placed it as an isolated lineage, basal to all other Oryzomyini.
Traits of O. hammondi that supported the latter placement include: a relatively short palate that does not extend behind the maxillary bones; simple posterolateral palatal pits; absence of a capsular process (a raising of the bone of the mandible, or lower jaw, at the back end of the incisor); and presence of the posteroloph on the upper third molar (a crest at the back of the tooth). In these characters, O. hammondi differs from many or most Oryzomyini and is similar to some species outside Oryzomyini, but all traits of O. hammondi are present in at least one other member of the tribe. Traits shared by O. hammondi and Oecomys included: tail with the same coloration above and below (unicolored); parietal bones extending to the sides of the skull; narrow zygomatic plate, without a zygomatic notch; posteroloph present on upper third molar; mesoflexus (a valley in the molar crown in front of the mesoloph crest) on upper second molar not divided in two.
In Weksler's analysis, species placed in Oryzomys did not form a coherent (monophyletic) group, but instead were found at various positions across the oryzomyine tree, and he suggested that most of these species, including O. hammondi, should be placed in new genera. Later in 2006, Weksler and others described ten new genera for species formerly placed in Oryzomys, including Mindomys for hammondi. Noting its "enigmatic distribution" and uncertain but perhaps basal position within Oryzomyini, they labeled the species an "extraordinary rat" worthy of continued inquiry. The generic name refers to Mindo, the type locality of M. hammondi.
Mindomys is now one of about 28 genera in the tribe Oryzomyini, which includes well over a hundred species distributed mainly in South America, including nearby islands such as the Galápagos Islands and some of the Antilles. Oryzomyini is one of several tribes recognized within the subfamily Sigmodontinae, which encompasses hundreds of species found across South America and into southern North America. Sigmodontinae itself is the largest subfamily of the family Cricetidae, other members of which include voles, lemmings, hamsters, and deermice, all mainly from Eurasia and North America.