Invasion of Dzungar Khanate and Qing

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Dzungar is a nation established by a tribe of Oirat, the Western Mongolian and it was based on Dzungar Basin and Ili River Vallay. Dzungar is called 'The Last Nomadic Empire' as the nomadic and equestrian people was splurged the devastating might abdicated from the main stream of the history after the empire disappeared.
During the reign of Galdan, the third Khan of Dzungar Khanate, the empire expanded the territory widely. Galdan was identified as a reincarnation of a high priest and spent his childhood with Dalai Lama the fifth, but on the death of his brother, Khan the second, he returned to secular life to be Khan of Dzungar Khanate. The hierarch of Dzungar believed in Tibetan Buddhism and this is why it is said that there was a religious side in the war with Qing that would occur later.
Galdan made the sovereign abdicated on seizure of Tarim Basin and kidnapped him to Ili as well as the Khoja of Ishaqis. Instead Galdan took Abdul Rashid as a puppet Khan to shift the hegemony to Afaqis. Thus oasis cities in Tarim Basin was subordinated to Dzungar Khanate.
The family of Moghulistan Khan was wiped out in 1697 and the throne was given to Afaqis. The throne was shifted from the descendants of Genghis to the descendants of Muhammad. There is a theory that objectify that this situation in which the religious authority has hegemony as well is the exceptional 'Holy Islam State' since the Islamic Empire.

Qing's full scale administration over Western Regions started in 1716, when reclamations were set in Dunhang, Kumul (Hami) and Barkol. Qianlong Emperor annihilated Dzungar Khanate in 1755, after having offensive and defensive fight repeatedly. There was a conspiration from Amursana, the military commander of Dzungar. However, as Amursana's expectation of acceding the position of Khan was not fulfilled, he rebelled against Qing Dynasty.
In 1757, Qing sent a battalion to exterminate the Dzungar considering Amursana's action betrayal and Dzungar is the land of barbarians that could not be moralized. Dzungar was annihilated by this and also the smallpox brought from Qing.
In Tarim Basin the Khoja brothers (Big Khoja and Small Khoja) countervailed. Qing, that captured Dzungar also captured this area. The Khoja brothers eloped to Badakhstan (Afghanistan) but got seized and killed there. All the kins of the brothers migrated to Beijing.
Qing, getting the Dzungar Basin and Tarim Islamic area, put them together and called it 'Xinjiang' (New Territory).

The way Qing Dynasty governed there was to let the Uyghurs serve under the Ministries and Generals as chiefs of each city. It was close to autonomous region. As the governance of Tibet was done similar way, it is considered as a preferential treatment to make Tibetan and Uyghur side on, as the Emperor, Manchu the minority, had to control overwhelming majority, the Han. As the dominance above shows, East Turkistan had peace in early nineteenth century and it lasted for about sixty years.

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