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.
Some native freshwater fish inhabit Puerto Rico, but some species, introduced by humans, have established populations in reservoirs and rivers.
[6] Rock samples from Sierra Bermeja in southwestern Puerto Rico, dated to the late Jurassic/early Cretaceous period, confirm this theory.
[7] 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.
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.
[9] 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.
Puerto Rico's transformation from a dry savanna environment to its present moist, forested state led to mass extinctions, especially of the vertebrate fauna.
[13] Fossil records show the existence of one shrew (Puerto Rican shrew, Nesophontes edithae), one sloth (Puerto Rican sloth),[14] three additional leaf-nosed bats (Macrotus waterhousii, Monophyllus plethodon, and Phyllonycteris major),[15] and five rodents (one giant hutia: Elasmodontomys obliquus, one hutia: Isolobodon portoricensis and three spiny rats: Heteropsomys antillensis, Heteropsomys insulans, and Puertoricomys corozalus).
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.
For example, the small Asian mongoose (Herpestes javanicus) 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.
[19] The animal became a Puerto Rican cultural, as well as scientific, icon when Tony Croatto wrote a song titled "Moisés".
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.
Bats play an important role in forest and cave ecology in Puerto Rico and help control mosquito populations.
[24] The South American families occurring in the Greater Antilles are the hummingbirds (Trochilidae), tyrant flycatchers (Tyrannidae), bananaquit (Coerebidae) and tanagers (Thraupidae), all of which are represented in Puerto Rico.
The prevailing theory suggests that bird fauna colonized the West Indies by transoceanic dispersal during the glacial periods of the Pleistocene.
[26] With a population of 13 individuals in 1975, the Puerto Rican parrot almost became the seventh, but conservation efforts helped save the species from extinction.
The majority of West Indian terrestrial reptile clade is believed to have arrived by flotsam dispersion from South America.
[27] Other terrestrial herpetofauna are believed to have arrived to the West Indies (and Puerto Rico) by the same method and subsequently undergone vicarization by banks or islands.
[30] The anole lizards of Puerto Rico, and the Greater Antilles in general, represent an interesting case of adaptive radiation.
The purposes of intentional introductions have been sport fishing for recreation and food, mosquito control, and to provide baitfish for largemouth bass.
[38] Sea breams (Archosargus rhomboidalis) and yellowfin mojarras (Gerres cinereus) are some of the species commonly found in mangrove habitats.
[44] Theotima minutissima, a small spider species found in abundance in the Caribbean National Forest, is believed to be parthenogenetic, meaning that it reproduces without fertilization by a male.
This animal competes with the endangered Puerto Rican parrot for secondary nesting cavities at the Caribbean National Forest.
Africanized bees, which pose an even greater threat for secondary cavity nesters, have recently extended their range to Puerto Rico.
Significant declines in the populations and diversity of the islands fauna are believed to have begun after the arrival of European settlers in the sixteenth century.
Habitat destruction, primarily as a result of forest clearing for sugar cane plantations, had a devastating effect on Puerto Rican fauna during the latter half of the nineteenth century.
Furthermore, human-introduced species such as rats, cats, the small Asian mongoose, and the cane toad have had a profound effect on the native fauna of Puerto Rico.
Rats on Monito Island are believed to be a limiting factor on the abundance of the endemic Monito gecko,[52] feral cats on Mona Island have been documented attacking common ground doves and endemic reptiles, and have been associated with the reduction of Mona ground iguana juveniles,[53] and mongooses have been documented preying on Puerto Rican parrot fledglings.
[58] The Department of Natural Resources of Puerto Rico maintains 25 areas with marine components but only two of these (11 km2) are designated as no-take zones.