DIVERSITY & ENDEMISM
Japan is home to roughly 5,600 species of vascular plants, about a third of which (1,950 species) are believed to be endemic. On Ogasawara-shoto, there are about 500 native plant species, of which 43 percent are endemic. Japan also has three endemic plant families (Sciadopityaceae, Glaucidiaceae, and Pteridophyllaceae), and about 20 endemic genera, seven of which are represented only by single species.
About 90 of Japan's native plant genera are considered part of the Arcto-Tertiary Geoflora; plant genera in this group (such as Wisteria and Buckleya) represent ancient lineages that were distributed around the world in the Tertiary Period. The once widespread forests that are home to these genera are now very fragmented, with members of this group having one or more species in two or three disparate parts of the world: southeastern North America, Japan and China. The origins of this odd biogeographic pattern have been a source of speculation since it was discovered nearly 200 years ago.
Prior to the opening of the Sea of Japan some 15 million years ago, the islands that now make up Japan were part of the Asian mainland. Perhaps not surprisingly then, the plant genera that are considered characteristic of the Japanese flora are rather poorly represented on nearby Taiwan, Province of China, with Japan's flora having come mostly from east-central China, Korea, and the islands and mainland to the north, whereas Taiwan's came from the Philippines and southeastern China.
Among Japan's notable plants are a number of rare, endemic species that are well-known favorites in gardens, both in Japan and around the world in temperate climates. These include Shirane-aoi (Glaucidium palmatum), which has large blue-purple, sometimes white, flowers, and Togakushisgouma (Ranzania japonica), found only in the high mountains from central to northern Honshu. Urahagusa (Hakonechloa macra), a rare local grass that grows in wet, rocky cliffs in the Tokai region of Japan, is a favorite pot and garden plant.
Nearly 370 bird species are known to occur regularly in Japan, although only 13 are endemic. The Okinawa woodpecker (Sapheopipo noguchii, CR) is the only representative of an endemic genus as is the Bonin white-eye (Apalopteron familiare, VU). Found in the Yanbaru Forest in the northern quarter of Okinawa Island, the Okinawa woodpecker was close to extinction in the 1930s, but has recovered to a population of about 146 to 584 birds. Another of the hotspot's well-known endemic birds is the Okinawa rail (Gallirallus okinawae, EN), which is also confined to Yanbaru. It is thought that only about 900 pairs of this bird survive in the wild. It is still threatened due to logging and alien invasive species. Three Endemic Bird Areas, as defined by BirdLife International, are found within Japan.
Japan also supports some important waterbird populations, including populations of the red-crowned crane (Grus japonensis, EN), resident on Hokkaido. About 85 percent of the world's hooded cranes (G. monacha, VU) and 40 percent of white-naped cranes (G. vipio, VU) winter at Izumi on Kyushu.
Tragically, Japan has already suffered a crisis of bird extinctions, with a number of species from its southern islands having been lost over the last two centuries. These include the Ryukyu pigeon (Columba jouyi) and Bonin wood-pigeon (C. Versicolor), the Bonin thrush (Zoothera terrestris), and the Bonin grosbeak (Chaunoproctus ferreorostris), a monotypic genus. All four of these extinctions were driven primarily by the introduction of exotic species, in particular of rats and cats.
Japan is home to only around 90 species of mammals, but about half of these are endemic to the hotspot. Sado Island, an island less than 1,000 km² off western Honshu, has two endemic mammals, the Sado shrew (Sorex sadonis, CR) and the Sado mole (Mogera tokudae, EN). There are also six endemic genera of mammals, including three that are monotypic: the Amami rabbit (Pentalagus furnessi, VU), found in the Amami-shoto in the Nansei-shoto, the Japanese dormouse (Glirulus japonicus, EN), found on Honshu and Shikoku, and the Ryukyu long-tailed giant rat (Kiplothrix legatus, EN), restricted to the Ryukyu Islands and the Yanbaru Forest on Okinawa. The Amami rabbit suffered a dramatic decline in the early twentieth century, subsequent to which it was declared a national monument and given complete legal protection, although sadly this protection did not extend to protection of its habitat. Habitat fragmentation and introduced mongooses threaten the rabbit's survival, and only about 2,500 individuals remain.
One of the best-known mammals in Japan is the Japanese macaque (Macaca fuscata), the most northerly-living monkey in the world, found on Honshu, Shikoku, Kyushu and a few other small islands. These are the famous "snow monkeys" that can be seen playing in the winter snow and warming up in volcanic springs. Another endemic macaque species, the Yaku-shima macaque (M. yakui) is found only on the island of Yaku-shima. The Iriomote cat (Prionailurus iriomotensis), restricted to Iriomote-jima, was first described in 1967, although it may be a subspecies of the leopard cat (P. bengalensis). There are no more than perhaps 100 individuals left on Iriomote-jima.
Japan has over 65 reptile species, almost 30 of which are endemic. The reptile fauna includes a number of important threatened species: the Okinawa black-breasted leaf-turtle (Geoemyda japonica, EN), the Kikuzato's brook snake (Opisthotropis kikuzatoi, CR), found only on the Kume-jima in the Okinawashoto in the Ryukyus, the Amami takachiho snake (Achalinus werneri, VU), confined to Amami, and the Tokashiki ground gecko (Goniurosaurus kuroiwae, VU), from the Ryukyus.
Endemism is particularly high among amphibians, with 44 of 50 species found only in Japan. The amphibian genus Hynobius is very well represented, with about 15 of the 25 known species worldwide being endemic to the hotspot, one of which, the Oki salamander (H. okiensis, CR), is confined entirely to Dogo, of the Okino-shima in Shimane Prefecture. The Japanese giant salamander (Andrias japonicus), found in western Honshu, Shikoku and Kyushu, can grow to more than one meter in length and is one of the world�s largest amphibians. Once threatened by human consumption, the salamander is now considered a natural monument and protected by law.
The hotspot has a relatively small freshwater fish fauna, with almost 215 native species, more than 50 of which are endemic. While most inland waters are dominated by fishes entering from the sea, there is also a significant representation of strictly freshwater groups, including minnows (Cyprinidae) and loaches (Cobitidae and Balitoridae) that have diversified within the hotspot and account for nearly half of the endemic species and three of four endemic genera. The occurrence of five lampreys and four sturgeons from ancient lineages mean that Japan also holds a disproportionately large amount of the evolutionary history of fishes.
Some invertebrate groups are very well documented in Japan. For example, nearly 240 butterfly species are thought to be native to Japan (although this includes naturalized species), and nearly 25 species of tiger beetles are recorded from the hotspot (about a quarter of which are endemic).