However, it is still one of the ten most critically endangered birds in the world. 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. At least six endemic species have become extinct in the last millennia: Puerto Rican Barn Owl ( Tyto cavatica), Puerto Rican Caracara ( Polyborus latebrosus), Puerto Rican Conure ( Aratinga chloroptera maugei), Puerto Rican Woodcock ( Scolopax anthonyi), Puerto Rican Quail-Dove ( Geotrygon larva), and the Antillean Cave Rail ( Nesotrochis debooyi).

The species is believed to have become extinct as a result of habitat alteration after the Wisconsin glaciation. For example, fossil evidence was discovered for a species of swift, Tachornis uranoceles, dated to the late Pleistocene (between 17,000 and 21,000 years ago). Puerto Rico's avifauna has diminished due to extinction and extirpation, either by natural forces or human intervention. The most primitive West Indies birds are the Todies which have an endemic representative in Puerto Rico, the Puerto Rican Tody. The prevailing theory suggests that bird fauna colonized the West Indies by transoceanic dispersal during the glacial periods of the Pleistocene. 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 avifauna of the West Indies is predominantly of tropical North American (southern North America and Central America) origin with aggressive South American species having colonized the area only recently. Approximately 120 species, including both native and introduced, breed regularly in the archipelago.

Almost half of the species (166) are accidental, meaning that they have been sighted only once or twice, and 42 of the species have been introduced, either directly or indirectly (mainly through habitat alteration), by humans. The avifauna of Puerto Rico is composed of 349 species, 18 of which are endemic to the archipelago.

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