The fauna of Puerto Rico is similar to other island archipelago faunas, with high endemism, and low, skewed taxonomic diversity. Bats are the only extant native terrestrial mammals in Puerto Rico. All other terrestrial mammals in the area were introduced by humans, and include species such as cats, goats, sheep, the small Indian mongoose, and escaped monkeys. Marine mammals include dolphins, manatees, and whales. Of the 349 bird species, about 120 breed in the archipelago, and 47.5% are accidental or rare.

The most recognizable and famous animal of Puerto Rico is probably the common coquí, a small endemic frog, and one of the 86 species that constitute Puerto Rico's herpetofauna. Some native freshwater fish inhabit Puerto Rico, but some species, introduced by humans, have established populations in reservoirs and rivers. The low richness-high diversity pattern is also apparent among invertebrates, which constitutes most of the archipelago's fauna.

The arrival of the first people about 4,000 years ago and of Europeans more than 500 years ago, had a significant effect on Puerto Rico's fauna. Hunting, habitat destruction, and the introduction of non-native species to Puerto Rico led to extinctions and extirpations (local extinctions). Conservation efforts, the most notable being for the Puerto Rican parrot, began in the second half of the 20th century. According to IUCN, as of 2002, there were 21 threatened species in Puerto Rico: two mammals, eight breeding birds, eight reptiles, and three amphibians.

Origin of Puerto Rican fauna

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". Geologically, the archipelago of Puerto Rico is young, having formed about 135 Ma (million years) ago. The prevailing hypothesis, proposed by Howard Meyerhoff, posits that the Puerto Rican Bank, consisting of Puerto Rico, its outlying islands, and the Virgin Islands with the exception of St. Croix, was formed from volcanism in the Cretaceous Period. Rock samples from Sierra Bermeja in southwestern Puerto Rico, dated to the late Jurassic/early Cretaceous period, confirm this theory.

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 vicariance 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 vicariant 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.Woods, C. A. (1989). "A new capromyid rodent from Haiti:the origin, evolution, and extinction of West Indian rodents, and their bearing on the origin of New World hystricognaths". In C. C. Black and M. R. Dawson (eds.), Papers on fossil rodents in honor of Albert Elmer Wood. Nat Hist. Mus. Los Angeles County Sci. Ser. 33:59–90.

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 vicariated lines would have begun.

The last major changes in Puerto Rican fauna occurred about 10,000 years ago as a result of the post-Ice Age rise in sea level and associated environmental changes. Puerto Rico's transformation from a dry savanna environment to its present moist, forested state led to mass extinctions, especially of the vertebrate fauna. Around this time, the Puerto Rican Bank—a single landmass comprising the archipelago of Puerto Rico (except for Mona, Monito and Desecheo) and the Virgin Islands (except for St. Croix)—became separated. The Puerto Rican Bank has never been connected to its closest eastern bank, St. Maarten.

Mammals

The richness of mammals in Puerto Rico, like many other islands, is low relative to mainland regions. The present-day native terrestrial mammal fauna of Puerto Rico is composed of only 13 species, all of which are bats. 18 marine mammals, including manatees, dolphins and whales, occur in Puerto Rican waters. Fossil records show the existence of one shrew (Puerto Rican shrew, Nesophontes edithae), one sloth (Puerto Rican sloth),Some authorities recognize two species of sloths occurring in Puerto Rico, the greater Puerto Rican sloth (Acratocnus major) and the lesser Puerto Rican sloth (Acratocnus odontrigonus). three additional leaf-nosed bats (Macrotus waterhousii, Monophyllus plethodon, and Phyllonycteris major),G. Morgan (2001). "Patterns of Extinction of West Indian Bats", pp. 369–408 in Biogeography of the West Indies: Patterns and Perspectives. Boca Raton, Florida, . and five rodents (one giant hutia: Elasmodontomys obliquus, one hutia: Isolobodon portoricensis and three spiny rats: Heteropsomys antillensis, Heteropsomys insulans, and Puertoricomys corozalus).C. A. Woods, R. Borroto Paéz and C. W. Kilpatrick. (2001). "Insular Patterns and Radiations of West Indian Rodents", pp. 335–353 in Biogeography of the West Indies: Patterns and Perspectives. Boca Raton, Florida, . Woods suggests a reason for their extinction: "Taxa evolving in isolation on oceanic islands without competition or predators may not be able to adapt to rapidly changing conditions, such as the extensive climatic fluctuations of the Ice Ages or sudden competition or predation from introduced animals".Woods, C. A. (1990). "The fossil and recent land mammals of the West Indies: an analysis of the origin, evolution, and extinction of an insular fauna", pp. 641–680 in International symposium on biogeographical aspects of insularity. Rome, Italy.

Other terrestrial mammals have been introduced throughout the history of Puerto Rico. Indigenous settlers first introduced dogs and guinea pigs from South or Central America. Afterwards, Taínos introduced hutias as a food source from Hispaniola. When the Spanish colonized the island in the early 16th century, they introduced domesticated animals such as dogs, cats, goats, pigs, cattle, horses, and donkeys. Other species such as black rats (Rattus rattus), Norway rats (Rattus norvegicus) and house mice (Mus sp.) have been unintentionally introduced as stowaways, possibly since Christopher Columbus's arrival in 1493. More recently, species have been introduced as a means of biological pest control. For example, the small Indian mongoose (Urva auropunctata) was introduced in the 19th century to control the damage caused by rats in sugar cane plantations. The introduction was a failure: the mongoose failed to control the rat population and instead contributed to the decline of native fauna such as the yellow-shouldered blackbird and possibly the elfin-woods warbler.

As part of a study on adaptation, 57 rhesus macaques (Macaca mulatta) were introduced to the island of Desecheo and other southern off-shore islands and cays in 1967. Prior to the introduction, Desecheo was the largest nesting colony of the brown booby, but mainly as a result of egg predation by the introduced macaques, no bird species presently nests in the island. Efforts to trap and remove the species have been unsuccessful and it has expanded its range to southwestern Puerto Rico. Other primates also have established populations in Puerto Rico. As a result of vandalism, 107 squirrel monkeys escaped from a research station at Sabana Seca in the late 1970s. The latest estimate for this population is 35 individuals.

Arguably the best known of aquatic mammals occurring in Puerto Rican waters is the Antillean manatee (Trichechus manatus manatus) which is listed as vulnerable by the IUCN. The archipelago's waters are one of the species' main breeding areas. Manatees gathered local media attention when a two-month manatee nicknamed Moisés was rescued and raised for 27 months by the Caribbean Stranding Network (CSN). Moisés was the first successful release of an orphaned, captive-raised manatee to the marine environment in the Caribbean. The animal became a Puerto Rican cultural, as well as scientific, icon when Tony Croatto wrote a song titled "Moisés". A municipality of Puerto Rico, Manatí is believed to be named after the species.

Puerto Rico's waters are also an important breeding site for the humpback whale during the Northern Hemisphere's winter. Humpback whale watching is a popular tourist attraction in the municipality of Rincón in western Puerto Rico.

Bats Extant bats of Puerto Rico belong to five families (Noctilionidae, Mormoopidae, Phyllostomidae, Vespertilionidae, and Molossidae) and include a total of 13 species, of which six subspecies are endemic to the archipelago. Seven of the 13 species are insectivores, four can be considered frugivores, one species feeds on nectar and another on fish. The species total is a relatively low number in comparison to the other Greater Antilles. Jamaica, for example, with an area approximately 1.2 times that of Puerto Rico, has 21 species (1.6 times that of Puerto Rico). A possible explanation for this is the comparatively large distance between the archipelago and the mainland dispersion areas. Jamaica, for example, is closer to Cuba and Hispaniola which are themselves closer to the mainland dispersion areas of North and Central America.

Bats play an important role in forest and cave ecology in Puerto Rico and help control mosquito populations. Most species (10 of 13) are cave-dwellers with low reproductive rates; the area with the highest species richness is the Caribbean National Forest, where eleven species occur. The red fig-eating bat (red fruit bat), endemic to the Puerto Rican Bank, plays an important role in the ecology of tabonucoTabonuco or Dacryodes excelsa. forest in the Luquillo Mountains since it is believed to be the only seed disperser of bulletwood (Manilkara bidentata). Cave ecosystems are enhanced by bat feces (guano) since many of the invertebrate cave fauna are either guano scavengers, detritivores or predators of the former two.

The bat species that occur in the archipelago of Puerto Rico are: greater bulldog bat (Noctilio leporinus), Antillean ghost-faced bat (Mormoops blainvillii), Parnell's mustached bat (Pteronotus parnellii), sooty mustached bat (Pteronotus quadridens), Jamaican fruit bat (Artibeus jamaicensis), Antillean fruit bat (Brachyphylla cavernarum), buffy flower bat (Erophylla sezekorni bombifrons), Leach's single leaf bat (Monophyllus redmani), red fruit bat (Stenoderma rufum), big brown bat (Eptesicus fuscus), eastern red bat (Lasiurus borealis), velvety free-tailed bat (Molossus molossus), and Mexican free-tailed bat (Tadarida brasiliensis).

Birds