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Prehistory and ancient history: A Paleolithic culture around 30,000 BC constitutes the first known habitation of the Japanese archipelago. This was followed from around 14,000 BC (the start of the Jōmon period) by a Mesolithic to Neolithic semi-sedentary hunter-gatherer culture, who include ancestors of both the contemporary Ainu people and Yamato people, characterized by pit dwelling and rudimentary agriculture. Decorated clay vessels from this period are some of the oldest surviving examples of pottery in the world. Around 300 BC, the Yayoi people began to enter the Japanese islands, intermingling with the Jōmon. The Yayoi period, starting around 500 BC, saw the introduction of practices like wet-rice farming, a new style of pottery, and metallurgy, introduced from China and Korea. Japan first appears in written history in the Chinese Book of Han. According to the Records of the Three Kingdoms, the most powerful kingdom on the archipelago during the 3rd century was called Yamataikoku. Buddhism was first introduced to Japan from Baekje of Korea, but the subsequent development of Japanese Buddhism was primarily influenced by China. Despite early resistance, Buddhism was promoted by the ruling class and gained widespread acceptance beginning in the Asuka period (592–710).

The Nara period (710–784) of the 8th century marked the emergence of a strong Japanese state, centered on an imperial court in Heijō-kyō (modern Nara). The Nara period is characterized by the appearance of a nascent literature as well as the development of Buddhist-inspired art and architecture. The smallpox epidemic of 735–737 is believed to have killed as much as one-third of Japan's population.[30] In 784, Emperor Kammu moved the capital from Nara to Nagaoka-kyō before relocating it to Heian-kyō (modern Kyoto) in 794.

Byōdō-in (1053) is a temple of Pure Land Buddhism. It was registered to the UNESCO World Heritage Site.This marked the beginning of the Heian period (794–1185), during which a distinctly indigenous Japanese culture emerged, noted for its art, poetry and prose. Lady Murasaki's The Tale of Genji and the lyrics of Japan's national anthem Kimigayo were written during this time.

Buddhism began to spread during the Heian era chiefly through two major sects, Tendai by Saichō, and Shingon by Kūkai. Pure Land Buddhism (Jōdo-shū, Jōdo Shinshū) greatly becomes popular in the latter half of the 11th century.

Feudal era

Japan's feudal era was characterized by the emergence and dominance of a ruling class of warriors, the samurai. In 1185, following the defeat of the Taira clan, sung in the epic Tale of Heike, samurai Minamoto no Yoritomo was appointed shogun and established a base of power in Kamakura. After his death, the Hōjō clan came to power as regents for the shoguns. The Zen school of Buddhism was introduced from China in the Kamakura period (1185–1333) and became popular among the samurai class.The Kamakura shogunate repelled Mongol invasions in 1274 and 1281, but was eventually overthrown by Emperor Go-Daigo. Go-Daigo was himself defeated by Ashikaga Takauji in 1336.

Ginkaku-ji in Kyoto (Higashiyama period in Muromachi Period, c. 1489). It was registered as part of the UNESCO World Heritage Site "Historic Monuments of Ancient Kyoto".Ashikaga Takauji establishes the shogunate in Muromachi, Kyoto. It is a start of Muromachi Period (1336–1573). The Ashikaga shogunate receives glory in the age of Ashikaga Yoshimitsu, and the culture based on Zen Buddhism (art of Miyabi) has prospered. It evolves to Higashiyama Culture, and has prospered until the 16th century. On the other hand, the succeeding Ashikaga shogunate failed to control the feudal warlords (daimyo), and a civil war (the Ōnin War) began in 1467, opening the century-long Sengoku period ("Warring States"). During the 16th century, traders and Jesuit missionaries from Portugal reached Japan for the first time, initiating direct commercial and cultural exchange between Japan and the West. Oda Nobunaga conquered many other daimyo using European technology and firearms; after he was assassinated in 1582, his successor Toyotomi Hideyoshi unified the nation in 1590. Hideyoshi invaded Korea twice, but following defeats by Korean and Ming Chinese forces and Hideyoshi's death, Japanese troops were withdrawn in 1598.[34] This age is called Azuchi-Momoyama Period (1573–1603).

Tokugawa Ieyasu served as regent for Hideyoshi's son and used his position to gain political and military support. When open war broke out, he defeated rival clans in the Battle of Sekigahara in 1600. Ieyasu was appointed shogun in 1603 and established the Tokugawa shogunate at Edo (modern Tokyo). The Tokugawa shogunate enacted measures including buke shohatto, as a code of conduct to control the autonomous daimyo; and in 1639, the isolationist sakoku ("closed country") policy that spanned the two and a half centuries of tenuous political unity known as the Edo period (1603–1868).The study of Western sciences, known as rangaku, continued through contact with the Dutch enclave at Dejima in Nagasaki. The Edo period also gave rise to kokugaku ("national studies"), the study of Japan by the Japanese.