Oryzomys Capito

''Oryzomys'' is a genus of semiaquatic rodents in the tribe Oryzomyini living in southern North America and far northern South America. It includes eight species, two of which—the marsh rice rat (''O. palustris'') of the United States and '' O. couesi'' of Mexico and Central America—are widespread; the six others have more restricted distributions. The species have had eventful taxonomic histories, and most species were at one time included in the marsh rice rat; additional species may be recognized in the future. The name ''Oryzomys'' was established in 1857 by Spencer Fullerton Baird for the marsh rice rat and was soon applied to over a hundred species of American rodents. Subsequently, the genus gradually became more narrowly defined until its current contents were established in 2006, when ten new genera were established for species previously placed in ''Oryzomys''.

Species of ''Oryzomys'' are medium-sized rats with long, coarse fur. The upperparts are gray to reddish and the underparts white to buff. The animals have broad feet with reduced or absent ungual tufts of hair around the claws and, in at least some species, with webbing between the toes. The rostrum (front part of the skull) is broad and the braincase is high. Both the marsh rice rat and ''O. couesi'' have 56 chromosomes, lack a gall bladder, and have a complex penis (as is characteristic of the Sigmodontinae) with some traits that are rare among oryzomyines; these characteristics are unknown in the other species of this genus.

The habitat includes various kinds of wetlands, such as lakes, marshes, and rivers. ''Oryzomys'' species swim well, are active during the night, and eat both plant and animal food. They build woven nests of vegetation. After a gestation period of 21 to 28 days, about four young are born. Species of ''Oryzomys'' are infected by numerous parasites and carry at least three hantaviruses, one of which ( Bayou virus) also infects humans. Two, maybe three, species have gone extinct over the last two centuries and at least one other is endangered, but the widespread marsh rice rat and ''O. couesi'' are not threatened.

Taxonomy

''Oryzomys'' is one of about thirty genera within the tribe Oryzomyini, a diverse group of well over a hundred species, many of which were formerly also included in ''Oryzomys''. Oryzomyini is one of several tribes within the subfamily Sigmodontinae of the family Cricetidae, which includes hundreds of other species of mainly small rodents, distributed mainly in the Americas and Eurasia.

Within Oryzomyini, a 2006 phylogenetic analysis by Marcelo Weksler which used both morphological and DNA sequence data found some evidence that ''Oryzomys'' is most closely related to a group including ''Holochilus'', ''Lundomys'', and ''Pseudoryzomys''. Although analyses based on morphological and combined data supported this relationship, sequences of the ''Rbp3'' gene alone instead placed ''Oryzomys'' among a group that included ''Nectomys'', ''Sigmodontomys'', and a few other genera. In all analyses, ''Oryzomys'' appeared within clade D of Oryzomyini. The relationship between ''Oryzomys'' and the ''Holochilus'' group was supported by five synapomorphies (shared derived characters)—absence or reduction of both the hypothenar and interdigital pads; reduction of ungual tufts of hairs surrounding the claws; having the back margin of the zygomatic plate of the skull at the same level as the front of the first upper molar; and the anterocone (front cusp) of the first upper molar divided by an anteromedian fossette. The first three are adaptations to the semiaquatic lifestyle that ''Oryzomys'' and the members of the ''Holochilus'' group share, and may thus be examples of convergent evolution.

Circumscription

The name ''Oryzomys'' was introduced in 1857 by Spencer Fullerton Baird for the marsh rice rat (now ''Oryzomys palustris'') of the eastern United States,Baird, 1857, p. 482 which had been first described twenty years earlier by Richard Harlan.Musser and Carleton, 2005, p. 1144 The name combines the Greek ''oryza'' "rice" and ''mys'' "mouse" and refers to the feeding habits of the marsh rice rat.Schwartz and Schwartz, 2001, p. 192 Baird placed ''Oryzomys'' as a subgenus of the now-defunct genus ''Hesperomys'' and included only the marsh rice rat in it, a classification which was followed by Elliott Coues in 1874 and 1877. In 1890, ''Oryzomys'' was raised to generic rank, and in subsequent years numerous additional species were ascribed to it, many of which were soon moved to separate genera. In the 1898 ''Catalogus Mammalium'', Édouard Louis Trouessart listed 67 species of ''Oryzomys'', including some that are now placed in ''Calomys'', ''Necromys'', ''Thomasomys'', and other genera unrelated to ''Oryzomys''. Some of the new genera proposed were soon subsumed in ''Oryzomys'' again, and in ''The Families and Genera of Living Rodents'' (1941), John Ellerman listed ''Microryzomys'', ''Oligoryzomys'', ''Melanomys'', ''Nesoryzomys'', and ''Oecomys'' as synonyms of ''Oryzomys''Ellerman, 1941, p. 340 and included about 127 species in it. In 1948, Philip Hershkovitz suggested that other oryzomyines like ''Nectomys'' and ''Megalomys'' could as well be included in ''Oryzomys'', and Clayton Ray followed this suggestion in 1962.

Hershkovitz and Ray's classification was never widely followed, and from 1976 on authors started to reinstate some of the other groups lumped in ''Oryzomys'' as separate genera. The genus was reduced to 43 species (out of 110 in Oryzomyini) in the third edition (2005) of ''Mammal Species of the World'',Musser and Carleton, 2005, p. 900 but it was still not a natural, monophyletic group; rather, it mostly united those oryzomyines that lacked the conspicuous specializations of other genera.Weksler, 2006, p. 82 In 2006, Marcelo Weksler's comprehensive phylogenetic analysis produced further evidence that the genus was polyphyletic, as species of ''Oryzomys'' were dispersed all over the oryzomyine tree. He proposed that eleven new genera should be created to accommodate those species that were not closely related to the type species of ''Oryzomys'', the marsh rice rat;Weksler, 2006, p. 75 he considered other options that would require fewer new genera, but argued that that would result in less meaningful genus-level groups in Oryzomyini. Later in the same year, Weksler, Percequillo, and Voss created ten new genera—''Aegialomys'', ''Cerradomys'', ''Eremoryzomys'', ''Euryoryzomys'', ''Hylaeamys'', ''Mindomys'', ''Nephelomys'', ''Oreoryzomys'', ''Sooretamys'', and ''Transandinomys''—for species formerly placed in ''Oryzomys'' and placed six more species related to '' "Oryzomys" alfaroi'' in ''Handleyomys'' pending the description of more new genera for them. They left only five species in ''Oryzomys'', which was now finally a natural, monophyletic group. Because of subsequent taxonomic work, the number of species has since increased to at least eight.

Some problems remain: ?''Oryzomys pliocaenicus'', a Miocene fossil from Kansas, is of uncertain identity but may belong in '' Bensonomys'',Weksler, 2006, p. 87 and fossils from the Miocene of Oregon and Pliocene (Pleistocene) of Saskatchewan.

Species

The current concept of ''Oryzomys'' derives from the ''palustris-mexicanus'' group recognized within a much larger genus ''Oryzomys'' by Merriam (1901) and the ''palustris'' group proposed by Goldman (1918).Carleton and Arroyo-Cabrales, 2009, p. 116 Merriam recognized 21 species within his group, but Goldman consolidated them into eight—the marsh rice rat in the United States, '' O. couesi'' in far southern Texas, Mexico, and Central America, and six others with small distributions. In 1960, Raymond Hall united ''O. couesi'' and the marsh rice rat into a single species, ''Oryzomys palustris'', and thereafter, other localized forms were also included in ''O. palustris''.Musser and Carleton, 2005, p. 1147 Hershkovitz described another species in the group, '' O. gorgasi'' from Colombia, in 1970 and the next year he noted that '' O. dimidiatus'', previously classified as a ''Nectomys'', was similar to ''O. palustris''. After 1979, the marsh rice rat and ''O. couesi'' were again regarded as separate as a result of further work in Texas, where their ranges meet. While reviewing ''O. gorgasi'' in 2001, J. Sánchez H. and colleagues redefined and characterized the ''O. palustris'' group and listed ''O. couesi'', ''O. dimidiatus'', ''O. gorgasi'', and the marsh rice rat as its members; Guy Musser and Michael Carleton in the 2005 third edition of ''Mammal Species of the World'' additionally listed '' O. nelsoni'' from María Madre Island in western Mexico.

In 2006, Weksler and colleagues followed the 2001 definition by Sánchez and others for the restricted genus ''Oryzomys'', but added '' O. antillarum'' from Jamaica as a species. Carleton and Joaquin Arroyo-Cabrales reviewed ''Oryzomys'' from western Mexico in 2009 and in this context provided an extended diagnosis of ''Oryzomys''. They recognized eight species: the six previously mentioned plus '' O. albiventer'' and '' O. peninsulae''. Also in 2009, Robert Voss and Weksler identified the subfossil ''Oryzomys curasoae'' from Curaçao as an island population of ''O. gorgasi''.Voss and Weksler, 2009, p. 73 The next year, Delton Hanson and colleagues published a study using DNA sequence data from the cytochrome ''b'', interphotoreceptor retinoid-binding protein, and alcohol dehydrogenase 1 genes to assess relationships within ''Oryzomys''. They recommended that the marsh rice rat be split into two species and that ''O. couesi'' be split into four species on the basis of the observed sequence divergence and other data.

Merriam divided his ''palustris-mexicanus'' group in two "series" according to the color of the underparts (white or fulvous). Goldman divided his ''palustris'' group in two "sections"—a ''couesi'' section with ''O. couesi'' and six related species, and a ''palustris'' section with ''O. palustris'' only. He noted that the latter differed from the former in the generally darker, more brownish, longer fur, and larger sphenopalatine vacuities (openings in the mesopterygoid fossa, the gap behind the end of the palate).Goldman, 1918, p. 20 As Weksler's 2006 analysis included only ''O. couesi'' and the marsh rice rat among species of ''Oryzomys'' in the strict sense, he could not test those groups. Carleton and Arroyo-Cabrales concurred with Goldman's division, listing additional characters, and noted that the ''palustris'' group may be more semiaquatically adapted than the members of the ''couesi'' group are. In the latter, the fur is usually reddish-brown, as opposed to grayish-brown in the ''palustris'' group. Members of the ''couesi'' group have smaller sphenopalatine vacuities and a smaller sphenopalatine foramen, a foramen (opening) in the side of the skull above the molars, and a more highly developed anterolabial cingulum on the third lower molar (a crest at the front of the tooth). The hypothenar pad of the hindfoot, located on the sole far from the fingers, is present in the ''couesi'' group, but absent in the ''palustris'' group. Interdigital webbing may be more highly developed in the ''palustris'' group.Carleton and Arroyo-Cabrales, 2009 Using morphological data, Voss and Weksler found a closer relationship between ''O. couesi'' and ''O. gorgasi'' to the exclusion of ''O. palustris'', but with low confidence. The DNA sequence data of Hanson and colleagues supported a deep separation between the ''palustris'' and ''couesi'' groups, but a Costa Rican sample (assigned to ''O. couesi'') was about as distant from the two groups as they were from each other.

The genus currently includes the following species:

Description

''Oryzomys'' contains medium-sized, semiaquatically specialized oryzomyine rodents. They have long, coarse fur that is grayish to reddish on the upperparts and white to buff on the underparts. The marsh rice rat superficially resembles the introduced species black rat and brown rat, but has larger differences in color between the upper- and underparts. The vibrissae (whiskers) are short and the ears are small and well-haired. The tail is usually as long as or longer than the head and body and is sparsely haired, but the hairs on the lower side are longer than those above. Females have eight mammae, as in most oryzomyines. The hindfeet are broad and have the first and fifth digits notably shorter than the middle three. The upper surface is hairy, but the underside is naked and covered with small irregularities (squamae). The pads are generally poorly developed, as are the ungual tufts. Interdigital webbing may be present, but its development is variable within the genus.

The karyotype has been recorded in various populations of the marsh rice rat and ''O. couesi'' and is apparently stable within the genus at 56 chromosomes, with the fundamental number of chromosomal arms ranging from 56 to 60 (2n = 56, FN = 56–60). In both species, the stomach has the characteristic pattern of sigmodontines (unilocular-hemiglandular): it is not split in two chambers by an incisura angularis and the front part (antrum) is covered by a glandular epithelium. Furthermore, the gall bladder is absent, a synapomorphy of Oryzomyini.

''Oryzomys'' species have a large skull with a short rostrum and high braincase. The interorbital region, located between the eyes, is narrowest to the front and is flanked by well-developed beads at its margins. The zygomatic plate is broad and has a well-developed zygomatic notch at its front. The zygomatic arch is robust and contains a small but distinct jugal bone. The interparietal bone, part of the roof of the braincase, is narrow and short;Goldman, 1918, p. 19; Carleton and Arroyo-Cabrales, 2009, p. 116 its narrowness is a synapomorphy for ''O. couesi'' plus the marsh rice rat according to Weksler's analysis.Weksler, 2006, p. 131 The incisive foramina are long, with their back margin at the front of the first molars or further back. The palate is also long, extending beyond the back margin of the maxillary bone, and is perforated near the third molars by well-developed posterolateral palatal pits. There is no alisphenoid strut, an extension of the alisphenoid bone that in some other oryzomyines separates two foramina in the skull. The auditory bullae are large. The condition of the arteries in the head is highly derived. In the mandible (lower jaw), the coronoid process, a process at the back, is well developedGoldman, 1918, p. 19 and the capsular process, a raising of the mandibular bone housing the root of the lower incisor, is conspicuous.

As usual in oryzomyines, the molars are pentalophodont (have the mesolophs and mesolophids, accessory crests, well developed) and bunodont, with the cusps higher than the connecting crests. The cusps on the upper molars are arranged in two longitudinal series, not three as in the black and brown rats. The front cusps of the first upper and lower molar (anterocone and anteroconid, respectively) are broad and not divided completely by an anteromedian flexus or flexid. Behind the anterocone, the anteroloph (a smaller crest) is complete and separated from the anterocone. On both the second and third lower molars, the anterolophid (a crest on the inner front corner) is present, a putative synapomorphy of the genus. The first molars have additional small roots in addition to the main ones, so that the upper first molar has four and the lower has three or four roots.

As is characteristic of Sigmodontinae, the marsh rice rat and ''O. couesi'' have a complex penis, with the baculum (penis bone) displaying large protuberances at the sides. The outer surface of the penis is mostly covered by small spines, but there is a broad band of nonspinous tissue. The papilla (nipple-like projection) on the dorsal (upper) side of the penis is covered with small spines, a character these two species share only with ''Oligoryzomys'' among oryzomyines examined. On the urethral process, located in the crater at the end of the penis, a fleshy process (the subapical lobule) is present; it is absent in all other oryzomyines with studied penes except ''Holochilus brasiliensis''. Both traits are recovered as synapomorphies of ''O. couesi'' plus the marsh rice rat in Weksler's analysis.

Distribution, ecology, and behavior

The range of ''Oryzomys'' extends from New Jersey in the eastern United States through Mexico and Central America south to northwestern Colombia and east to northwestern Venezuela and Curaçao. Species of ''Oryzomys'' usually live in wet habitats such as marshes, streams, and mangroves, but both the marsh rice rat and ''O. couesi'' are also occasionally encountered in drier habitats. They occur or occurred on many continental-shelf islands and one oceanic island, Jamaica; their adeptness at colonizing islands may be caused by their close association with water and frequent occurrence in coastal wetlands. The oldest fossils date to the Rancholabrean of the United States, about 300,000 years ago; although there have been some earlier North American records, those are not in fact referable to ''Oryzomys'' or even Oryzomyini. Oryzomyines likely evolved in South America east of the Andes; the presence of ''Oryzomys'' in Central America and other trans-Andean regions is thought to be the result of one of several independent invasions of this region by oryzomyines.Weksler, 2006, p. 88 Alternatively, ''Oryzomys'' may have evolved from the Pliocene North American '' Jacobsomys''. ''O. antillarum'' may have reached Jamaica during the last glacial period while sea levels were low.

Behavior is known mainly from the marsh rice rat and ''O. couesi'', with some scattered data from the other species. ''Oryzomys'' are semiaquatic, spending much time in the water, and otherwise mainly live on the ground;Reid, 2009, p. 205 both the marsh rice rat and ''O. couesi'' are known to be excellent swimmers and will flee into the water when disturbed. Both are also active during the night and build nests of interwoven vegetation, which may be suspended above the water. Breeding may occur throughout the year in both species, but is known to be seasonally variable in the marsh rice rat. In both, gestation takes about 21 to 28 days and litter size is usually one to seven, averaging three to five. Young marsh rice rats and ''O. couesi'' become reproductively active when about 50 days old.

The marsh rice rat, ''O. couesi'', and ''O. gorgasi'' are known to be omnivores, eating both plant and animal material. They eat both seeds and green plant parts and consume a variety of animals, including insects, crustaceans, and many others. The barn owl (''Tyto alba'') is a major predator on the marsh rice rat and remains of ''O. antillarum'', ''O. couesi'', and ''O. gorgasi'' have been found in owl pellet deposits. Several other animals are known to prey on ''Oryzomys''. A variety of parasites are known from ''O. couesi'' and the marsh rice rat and two parasitic nematodes have been found in ''O. gorgasi''.

Human interactions

Two species of ''Oryzomys'', ''O. antillarum'' and ''O. nelsoni'', have gone extinct since the 19th century, and a third, ''O. peninsulae'', is unlikely to be still extant. Their extinction may have been caused by habitat destruction and by introduced species such as the small Asian mongoose