Contents of Oryzomyini
An oryzomyine group was first envisaged by Oldfield Thomas in the early 20th century. He defined it to include pentalophodont species, which have a mesoloph(id) on the upper and lower molars, with a long palate (extending past the third molars). Thomas included Oligoryzomys, Oecomys, and Oryzomys (which included many species now in other genera), as well as Rhagomys, which is currently classified in the related tribe Thomasomyini instead. In 1944, Hershkovitz proposed a more extended definition of the group, excluding Rhagomys, but including Nectomys (then including Sigmodontomys), Neacomys, and Scolomys. Some subsequent authors did not separate the oryzomyines from the thomasomyines, which were distinguished from them by having a short palate, including Vorontsov, who in 1959 was the first to use Oryzomyini as a formal family-group name. He included most current oryzomyines as well as the thomasomyines and tylomyines, which are now known to be more distantly related.
The genera Holochilus (including Lundomys at the time), Pseudoryzomys, and Zygodontomys were not included at the time because of their tetralophodont molars (lacking complete mesoloph(id)s); instead, Holochilus was considered to be a sigmodont, related to Sigmodon and Reithrodon, and Pseudoryzomys and Zygodontomys were considered to be members of Phyllotini, another large South American tribe. Although lacking mesoloph(id)s, these genera share other characters with oryzomyines, and a series of papers by Robert Voss and coworkers in the early 1990s established their membership in Oryzomyini.
In a 1993 paper, Voss and Carleton proposed the first cladistic diagnosis of Oryzomyini. They included twelve genera and proposed five synapomorphies for the tribe: presence of a pair of mammae on the chest; a long palate marked by posterolateral palatal pits, perforations near the third molar; absence of an alisphenoid strut, which in some sigmodontines separates two foramina (openings) in the skull; absence of a suspensory process of the squamosal bone attached to the roof of the tympanic cavity, the tegmen tympani; and absence of a gall bladder. Some of these have been reversed in some oryzomyines; for example, an alisphenoid strut is present in several oryzomyines, including Eremoryzomys.
The contents of Oryzomyini have been largely stable since, but the allocation of some animals has been contentious. Megaoryzomys, an extinct giant rat from the Galápagos Islands, has been allocated to both Oryzomyini and Thomasomyini, but its correct classification currently remains unclear. The genus Scolomys has been excluded from Oryzomyini on the basis of studies of the mitochondrial cytochrome b gene, but the nuclear IRBP gene provides evidence for its membership in Oryzomyini. Handleyomys fuscatus was placed in the thomasomyine genus Aepeomys before its close relationship to H. intectus was recognized in 2002. Microakodontomys transitorius was described as a transitional form between oryzomyines and akodontines, but later allied with Oryzomyini and even summarily dismissed as an anomalous Oligoryzomys.
In the early 2000s, the advent of molecular phylogenetics has led to progress in the understanding of the relationships of oryzomyines. They are currently classified in the family Cricetidae, which includes the voles, hamsters, deermice, and many other species, chiefly in the Americas and Eurasia. Within this family, they are part of the subfamily Sigmodontinae, which is mainly distributed in South America but also extends into southern North America. Sigmodontinae includes several tribes, most of which cluster into a clade now known as Oryzomyalia, which includes Oryzomyini, Akodontini, Phyllotini, Thomasomyini, and other, smaller groups, but not the cotton rats (Sigmodon) and the Ichthyomyini.
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.