Oryzomyini - Taxonomy - Internal Classification

Internal Classification

The relationships among the oryzomyine genera have long been obscure, although several studies provided insights into the relations of some genera. The single most significant problem in oryzomyine taxonomy has been the definition of the type genus, Oryzomys, which in one classification included all animals then recognized as oryzomyines. Many groups were later excluded from the genus, but even so it included forty species that did not form a monophyletic group.

In the 2000s, Marcelo Weksler published several studies in which he used evidence from IRBP, a nuclear gene, and morphology to assess the relationships among the members of Oryzomyini. He provided support for several intergeneric relationships and clarified the scale of the Oryzomys problem, as species of Oryzomys appeared in about ten separate clades. In a 2006 publication, he and coworkers described ten new genera for species previously placed in Oryzomys and transferred some others to Handleyomys, leaving only about six species in Oryzomys.

Weksler's analyses suggested that oryzomyines fall into four major clades, which were largely congruent across his analyses of morphology and IRBP, but support for all of those was limited and the placement of some genera remained unclear. He dubbed these clades "clade A" through "clade D". Some analyses supported a relationship between clades C and D, which in turn were related to clade B, with clade A at a basal position, but other analyses could not resolve the relationships among the major clades. The four clades are as follows:

• Clade A includes only Scolomys and Zygodontomys, but support for a relationship between those morphologically and ecologically dissimilar genera was not strong.
• Clade B includes at least Oecomys, Handleyomys, Euryoryzomys, Transandinomys, Hylaeamys, and Nephelomys, the latter four of which were included in Oryzomys until 2006. Amphinectomys and Mindomys were also recovered in the clade in some analyses, but the former, for which most morphological characters are unknown, is more likely related to Nectomys within clade D and the relations of the latter, a poorly known yet unique animal, are obscure as some analyses suggest it is a basal member of Oryzomyini. There is little support for all intergeneric relationships within the clade.
• Clade C includes Oligoryzomys, Neacomys, Microryzomys, and Oreoryzomys, which was placed in Oryzomys until 2006. No intergeneric relationships within this clade received substantial support.
• Clade D includes Drymoreomys, Eremoryzomys, Cerradomys, Sooretamys, Oryzomys, Lundomys, Pseudoryzomys, Holochilus, Aegialomys, Nesoryzomys, Melanomys, Sigmodontomys, Nectomys, most likely Amphinectomys, and the extinct Megalomys, Agathaeromys, and Pennatomys. Eremoryzomys, Cerradomys, Sooretamys, and Aegialomys were included in Oryzomys before 2006. There is some support for a basal placement of Eremoryzomys within this clade and for two major groups of related genera, one including Holochilus, Lundomys, and Pseudoryzomys and the other Nectomys, Amphinectomys, Sigmodontomys, Melanomys, Aegialomys, and Nesoryzomys, with the extinct Megalomys and Pennatomys. The Holochilus–Lundomys–Pseudoryzomys group also includes the extinct Noronhomys and Carletonomys. Oryzomys may be its closest relative, but it is possible that this arrangement is the result of a convergent development of adaptations to a life in the water in the two groups. Within the group of Nectomys and related genera, there is some support for a core group that excludes Aegialomys and Nesoryzomys and for two subclades within the core group, one including Nectomys and Amphinectomys and the other Melanomys and Sigmodontomys.

The affinities of some species remain unclear. Many oryzomyines are known from the Lesser Antilles, including "Ekbletomys hypenemus" and species of Megalomys and Oligoryzomys, but most remain undescribed.