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The fauna of the Caribbean has a low high-level diversity and a high radiation of some taxa. At the genus level there is a 28% endemism while at the species level the endemism is 74%. Vertebrates are the most studied orgranims in the region with 1,295 described species.

Origin
The Caribbean Plate, an oceanic tectonic plate on which Puerto Rico and the Antilles (with the exception of Cuba) lie, was formed in the late Mesozoic. According to Rosen, when South America separated from Africa, a volcanic archipelago known as "Proto-Antilles" was formed. It later divided into the present-day Greater and Lesser Antilles because of a new fault line in the "Proto-Antilles". In the early Cenozoic the proto-Antilles collided and fused with the Bahamas platform.

There is ongoing debate over when and how the ancestors of vertebrate fauna colonized the Antilles—particularly whether the Proto-Antilles were oceanic islands or whether they once formed a land connection between South and North America. The first, and prevailing, model favors overwater dispersal from continental, primarily South American, fauna; the other suggests the vicarization of proto-Antillean fauna. Hedges et al. conclude that dispersal was "the primary mechanism for the origin of West Indian biota". Vertebrate terrestrial genera such as Eleutherodactylus dispersed in a "filter" effect among the islands before any vicarization event occurred. However, other fauna such as the endemic Antillean insectivores (Nesophontes sp., Solenodon marcanoi and others) and freshwater fish appear to have colonized the West Indies earlier through other means. Woods provides evidence to support this hypothesis by analyzing the arrival of ancestors of the Antillean capromyids and echimyids, concluding that an ancient echimyid must have arrived on the Greater Antilles from South America either by island-hopping through the Lesser Antilles or by rafting either to Puerto Rico or Hispaniola.

MacPhee and Iturralde provide an alternate hypothesis that the initiators of land mammal clades arrived on the Proto-Antilles by the mid-Tertiary period, approximately at the Eocene–Oligocene boundary. A short-lived (~1 Ma) landmass named "GAARlandia" (Greater Antilles + Aves Ridge land) connected northwestern South America with three of the Greater Antilles (Cuba, Hispaniola and Puerto Rico) during this period. Afterwards, during the fragmentation of the Proto-Antilles, divergence of vacariated lines would have begun.

The majority of terrestrial fauna dispersed or vicariated from South America. Some genus, such as the Tarentola lizards, are believed to have dispersed from Africa. The primary source of birds is Central and North America. Bats originated primarily in Central and South America. Fishes have a diverse origin with lineages from North, Central and South America.

Mammals
The diversity of mammals in the Caribbean is very low when compared against mainland regions. Excluding bats, nearly 90% of the mammals of the Caribbean faunal region have gone extinct since the late Pleistocene, including all the sloths and monkeys, the unique insectivore Nesophontes, two of four species of solenodon, and a variety of rodents including all giant hutias, leaving only a few hutia species extant.

Bats
There are 56 extant species of bats in the Caribbean; 28 of which are endemic. Overwater dispersal is the most accepted mechanism for the origin of Caribbean bats. The most common species are Monophyllus redmani, Brachyphylla cavernarum, Artibeus jamaicensis, Noctilio leporinus, Tadarida brasiliensis, and Molossus molossus.