Oryzomys peninsulae was first collected in 1896 and Oldfield Thomas described it in 1897 as a full species of Oryzomys.[5] It was retained as a distinct species related to O. couesi and O. palustris until 1971, when Philip Hershkovitz swept it, and other outlying populations of the same species group, as subspecies under an expanded concept of O. palustris.[6] Raymond Hall concurred in the second edition (1981) of Mammals of North America, arguing that O. peninsulae differed less from mainland Oryzomys populations (currently classified as O. couesi mexicanus) than some other forms he included in O. palustris differed from each other.[7] After studies of the contact zone between North American O. palustris and Central American O. couesi in southern Texas and northeastern Tamaulipas (by Benson and Gehlbach in 1979 and Schmidt and Engstrom in 1994) made clear that the two are distinct from each other, O. peninsulae remained as a subspecies of O. couesi.[6] In 2009, Michael Carleton and Joaquín Arroyo-Cabrales reviewed the classification of western Mexican Oryzomys and used morphological and morphometrical data to characterize four distinct Oryzomys species in the region. O. peninsulae and another isolated population, O. nelsoni from the Islas Marías, were both retained as separate species, as was O. albiventer from montane mainland Mexico. They kept the population in the coastal lowlands as a subspecies, O. couesi mexicanus, of Oryzomys couesi.
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