Mammal diversity in Chile, as in other parts of temperate South America, is low. It has been suggested that severe climatic conditions associated with Pleistocene glacial movements in the Andes may have had a strong impact in reducing the diversity of temperate mammal faunas in South America. Major faunal extinctions were also present in South America at the end of the Pleistocene, as in North America, and these extinctions have been associated with the arrival of early man.
Many ecological niches in temperate South America appear to be incompletely occupied by mammals in comparison with North America. Chile has a mammal fauna of 99 native terrestrial species, with 64 species occurring within the hotspot region. Five genera are endemic. The largest single group is the Rodentia, and comprises 60% of this total. Next in abundance are the Carnivora with 14%, and the Chiroptera (bats) with 10%. Large mammal species are particularly low in number. These include species of felids (puma, Geoffrey’s cat, and colo colo), three species of canids (all fox species of Pseudalopex), four camelids (guanaco, vicuna, and the domesticated llama and alpaca), and three cervids (huemul, northern huemul, and pudu). Mammal faunas of Chile have been placed into five biogeographic groupings: the summer rainfall Altiplano region of northeastern Chile, the Atacama Desert and adjacent winter rainfall Andes of northern Chile, the Andes of central Chile, the mediterranean-climate region of central Chile, the Austral forests of southern Chile, and the Patagonian region. The monito del monte (Dromiciops gliroides) forms an endemic family, the Microbiotheriidae.
In addition to these native mammal faunas, there are 15 species of terrestrial mammals that have become naturalized in Chile. Five of these occur only on the Juan Fernandez Islands, where they have had an extreme impact on the structure and composition of the native flora.
The total bird diversity of Chile is only moderate. Including the oceanic islands of Pascua and Juan Fernandez and the Antarctic territory claimed by Chile, there are reports of 451 native species and five introduced species for Chile. The hotspot area includes 226 species, with 12 of these being endemic. The biogeographical isolation of the Chilean bird fauna shows parallels with that of the mammal fauna in the manner in which niches have been filled in unusual manners. Corvids, for example, are absent from Chile. Their role as scavengers has been filled by caracaras.
There are 87 native species of terrestrial reptiles in Chile, divided among 7 families and 18 genera. These include six snakes (four genera) and 81 lizards (14 genera). For the hotspot boundaries, there are 41 reptile species, with 27 of these being endemic. The diverse lizard fauna of Chile is strongly dominated by the family Tropiuridae, in particular the iguanid genus Liolaemus. This diverse genus and its evolution have been the focus of a large number of ecological and evolutionary studies. The occurrence of distinctive populations within individual species has led to the designation of a large number of subspecies. There are two endemic species of snakes. The highest diversity of reptiles in Chile occurs in the northern desert and Andean areas, outside of the core mediterranean-climate region. This region is also the site of the greatest degree of endemism.
The amphibian fauna of Chile exhibits an unusually high level of endemism, in comparison with other vertebrate groups. There are 43 native species in the hotspot of Chile, with five of the 12 genera endemic. The highest diversity of these amphibians is located in the forested regions of south-central Chile. Notable for their absence are salamanders, with only frogs and toad species present. More than three quarters of the native frogs and toads are endemic to Chile. Many of these endemic species are quite rare and localized in distribution.
The native fish fauna for the Chilean hotspot region includes 43 species, including two endemic families.